void TestChunks::compare()
{
QByteArray rHighLighted;
QByteArray rData = _chunks.data(0, -1, &rHighLighted);
bool error = false;
if (rData != _data)
error = true;
if (rHighLighted != _highlighted)
error = true;
_tCnt += 1;
int chunkSize = _chunks.chunkSize();
QString tName = QString("logs/%1_%2_%3").arg(_tName).arg(_tCnt).arg(chunkSize);
if (error || (_tCnt >= _saveFile))
{
QFile file1(tName + "_data.txt");
file1.open(QIODevice::WriteOnly);
file1.write(_data);
file1.close();
QFile file2(tName + "_highlighted.txt");
file2.open(QIODevice::WriteOnly);
file2.write(_highlighted);
file2.close();
QFile file3(tName + "_rData.txt");
file3.open(QIODevice::WriteOnly);
file3.write(rData);
file3.close();
QFile file4(tName + "_rHighlighted.txt");
file4.open(QIODevice::WriteOnly);
file4.write(rHighLighted);
file4.close();
}
if (error)
{
qDebug() << "NOK " << tName;
*_log << "NOK " << tName << "\n";
}
else
{
qDebug() << "OK " << tName;
*_log << "OK " << tName << "\n";
}
}
void XMLParserTest::initTestCase(){
xmlParser = new XMLParser();
QString path = QString("%1/%2").arg(StandardPaths::writeableLocation());
QFile file(":/testData/transportations.xml");
if(file.open(QIODevice::ReadOnly)){
if(file.copy(path.arg("transportations.xml")))
QFile::setPermissions(path.arg("transportations.xml"), QFile::WriteOwner | QFile::ReadOwner);
}
file.close();
QFile file2(":/testData/equipments.xml");
if(file2.open(QIODevice::ReadOnly)){
if(file2.copy(path.arg("equipments.xml")))
QFile::setPermissions(path.arg("equipments.xml"), QFile::WriteOwner | QFile::ReadOwner);
}
file2.close();
QFile file3(":/testData/products.xml");
if(file3.open(QIODevice::ReadOnly)){
if(file3.copy(path.arg("products.xml")))
QFile::setPermissions(path.arg("products.xml"), QFile::WriteOwner | QFile::ReadOwner);
}
file3.close();
QFile file4(":/testData/employees.xml");
if(file4.open(QIODevice::ReadOnly)){
if(file4.copy(path.arg("employees.xml")))
QFile::setPermissions(path.arg("employees.xml"), QFile::WriteOwner | QFile::ReadOwner);
}
file4.close();
QFile file5(":/testData/workplaces.xml");
if(file5.open(QIODevice::ReadOnly)){
if(file5.copy(path.arg("workplaces.xml")))
QFile::setPermissions(path.arg("workplaces.xml"), QFile::WriteOwner | QFile::ReadOwner);
}
file5.close();
QFile file6(":/testData/workprocesslists.xml");
if(file6.open(QIODevice::ReadOnly)){
if(file6.copy(path.arg("workprocesslists.xml")))
QFile::setPermissions(path.arg("workprocesslists.xml"), QFile::WriteOwner | QFile::ReadOwner);
}
file6.close();
}
void DecisionTree::FlushIntoFile(){
if(__MESSAGE__)
cout << "Flushing..." << endl;
FlushVpidToFile(accTrain, "PruneTainAcc.csv");
FlushVpidToFile(accVal, "PruneValAcc.csv");
FlushVpidToFile(accTest, "PruneTestAcc.csv");
filebuf fb;
fb.open("PruneAllAcc.csv", ios::out);
ostream file4(&fb);
for(int i=0; i<accTest.size(); i++)
file4 << accTest[i].first << "," << accTrain[i].second << "," << accVal[i].second << "," << accTest[i].second << endl;
fb.close();
if(__MESSAGE__)
cout << "Flushing data into files finished ... " << endl;
}
int
main
(
int argc,
char** argv
)
{
JInitCore();
JString fileName;
if (!(JGetChooseSaveFile())->SaveFile("Save file as:", NULL, "junk", &fileName))
{
return 0;
}
ofstream file0(fileName);
file0 << "0123456789";
file0.close(); // force write to disk
fstream file1(fileName, kJTextFile);
cout << "Length of file (10): " << JGetFStreamLength(file1) << endl;
fstream* file2 = JSetFStreamLength(fileName, file1, 20, kJTextFile);
cout << "Old fstream open? (0) " << (file1.rdbuf())->is_open() << endl;
cout << "Length of file (20): " << JGetFStreamLength(*file2) << endl;
fstream* file3 = JSetFStreamLength(fileName, *file2, 5, kJTextFile);
cout << "Old fstream open? (0) " << (file2->rdbuf())->is_open() << endl;
cout << "Length of file (5): " << JGetFStreamLength(*file3) << endl;
file3->close();
ofstream file4(fileName);
file4.close();
file1.open(fileName, kJTextFile);
cout << "default open of ofstream should erase file" << endl;
cout << "Length of file (0): " << JGetFStreamLength(file1) << endl;
file1.close();
remove(fileName);
return 0;
}
void ThroughPut::InputManagement(){
//QFile file("datain.txt");
QFile file0("./Pilot_send_data/pilot_1200_im.txt");
if (!file0.open(QIODevice::ReadOnly | QIODevice::Text)){
qDebug() << file0.errorString();
qDebug() << "Last sentence is in QPSK Inputmanagement." << endl;
}
//qDebug() << QObject::tr("file text:") << endl << file.readAll();
//char str[100];
char str6[100];
for( int i = 0 ; i < 1200 ; i++ ){
file0.readLine(str6,100);
double crr = 0;
crr = char2int(str6);
//qDebug() << "pilot2[ "<< i <<"][0] is :"<<crr;
pilot2[i][1] = crr;
}
file0.close();
QFile file5("./Pilot_send_data/pilot_1200_re.txt");
if (!file5.open(QIODevice::ReadOnly | QIODevice::Text)){
qDebug() << file5.errorString();
qDebug() << "Last sentence is in QPSK Inputmanagement." << endl;
}
//qDebug() << QObject::tr("file text:") << endl << file.readAll();
//char str[100];
for( int i = 0 ; i < 1200 ; i++ ){
file5.readLine(str6,100);
double crr = 0;
crr = char2int(str6);
//qDebug() << "pilot2[ "<< i <<"][0] is :"<<crr;
pilot2[i][0] = crr;
}
file5.close();
//QFile file("./pilot4_send_data/pilot4_1200_re.txt");
QFile file("./16qam_data_new/data_im.txt");
if (!file.open(QIODevice::ReadOnly | QIODevice::Text)){
qDebug() << file.errorString();
qDebug() << "Last sentence is in ThroughPut Inputmanagement." << endl;
}
//qDebug() << QObject::tr("file text:") << endl << file.readAll();
//char str[100];
char str[100];
for( int i = 0 ; i < 1200 ; i++ ){
file.readLine(str,100);
double crr = 0;
crr = char2int(str);
//qDebug() << "pilot4[ "<< i <<"][0] is :"<<crr;
pilot4[i][0] = crr;
}
//qDebug() << "last one is :"<< ThroughPut[9][0] ;
file.close();
//QFile file2("./pilot4_send_data/pilot4_1200_im.txt");
QFile file2("./16qam_data_new/data_re.txt");
if (!file2.open(QIODevice::ReadOnly | QIODevice::Text)){
qDebug() << file2.errorString();
qDebug() << "Last sentence is in ThroughPut Inputmanagement." << endl;
}
//qDebug() << QObject::tr("file text:") << endl << file2.readAll();
//char str[100];
for( int i = 0 ; i < 1200 ; i++ ){
file2.readLine(str,100);
double crr = 0;
crr = char2int(str);
//qDebug() << "pilot4[ "<< i <<"][1] is :"<<crr;
pilot4[i][1] = crr;
}
//qDebug() <<"apsk[0][0] is :"<< *(pdata) << endl;
file2.close();
// QFile file3("./16qam_data/data_re.txt");
QFile file3("./16qam_data_new/data_re.txt");
if (!file3.open(QIODevice::ReadOnly | QIODevice::Text)){
qDebug() << file3.errorString();
qDebug() << "Last sentence is in ThroughPut Inputmanagement." << endl;
}
//qDebug() << QObject::tr("file text:") << endl << file.readAll();
//char str[100];
int cnt_2_500=0;
for( int i = 0 ; i < 600 ; i++ ){
file3.readLine(str,100);
double crr = 0;
if(i%6!=0){
crr = char2double(str);
// qDebug() << "re[ "<< i <<"][0] is :"<<crr;
qam16_3[cnt_2_500][0] = crr;
cnt_2_500++;
}
}
//qDebug() << "last one is :"<< ThroughPut[9][0] ;
file3.close();
// QFile file4("./16qam_data/data_im.txt");
QFile file4("./16qam_data_new/data_im.txt");
if (!file4.open(QIODevice::ReadOnly | QIODevice::Text)){
qDebug() << file4.errorString();
qDebug() << "Last sentence is in ThroughPut Inputmanagement." << endl;
}
//qDebug() << QObject::tr("file text:") << endl << file.readAll();
//char str[100];
int cnt_2_500_2;
for( int i = 0 ; i < 600 ; i++ ){
file4.readLine(str,100);
double crr = 0;
if(i%6!=0){
crr = char2double(str);
//qDebug() << "im[ "<< i <<"][0] is :"<<crr;
qam16_3[cnt_2_500_2][1] = crr;
cnt_2_500_2++;
}
}
//qDebug() << "last one is :"<< ThroughPut[9][0] ;
file4.close();
}
int main(int argc, char * argv[])
{
PARSE_ARGS;
////////////////////////////////////////////////////////////////////////////////////////////////////////Pipipeline 1////////////////////////////////////////////////////////////////////////////////////////////////////////////////
std::string nameFile;
nameFile="/biomed-resimg/work/mjacquem/Slicer3Thickness2/SampleBatchMake/dataset.csv";
std::ifstream Sub(nameFile.c_str(),std::ios::in);
int i=0;
if(Sub)
{
std :: string line;
while(getline( Sub, line ))
{ std :: cout <<"1"<<endl;
if (i>0)
{
char labelfile[200];
char subjid[100];
char WarpedCorrespondenceMesh[200];
char CorrespondenceMesh[200];
char labelMapInput[200];
char measurementOutput[200];
char group[100];
char ThicknessSamplingResult[200];
/*std :: string labelfile;
std :: string subjid;
std :: string WarpedCorrespondenceMesh;
std :: string CorrespondenceMesh;
std :: string labelMapInput;
std :: string measurementOutput;
std :: string group;
std :: string ThicknessSamplingResult;*/
std::string BatchMakeScriptFile = "slicer3ThicknessSPHARM.bms";
std::ofstream file( BatchMakeScriptFile.c_str());
readFileCSV(line, group,subjid,labelMapInput, measurementOutput,labelfile, CorrespondenceMesh, WarpedCorrespondenceMesh, ThicknessSamplingResult);
//std :: cout << "s is : " << group << std :: endl;
file <<"set (labelMapInput "<< labelMapInput<<")"<<std::endl;
file <<"set (measurementOutput "<< measurementOutput<<")"<<std::endl;
file <<"set (spharmBinaryInput "<<labelfile<<")"<<std::endl;
file <<"set (case1 "<< subjid <<")"<<std::endl;
file <<"set (group "<< group <<")"<<std::endl;
file <<"set (subjWorkDir "<< subjWorkDir<<")"<<std::endl;
file <<"set (exprId "<< exprId<<")"<<std::endl;
file <<"include (/biomed-resimg/work/mjacquem/Slicer3Thickness2/SampleBatchMake/ThicknessSpharm.bms)"<<std::endl;
file.close();
/*
bm::ScriptParser m_Parser;
m_Parser.LoadWrappedApplication( "/biomed-resimg/work/mjacquem/Slicer3Thickness2/SampleBatchMake/bmm2" );
m_Parser.SetBatchMakeBinaryPath( "/biomed-resimg/work/mjacquem/Slicer3Thickness2/SampleBatchMake/bmm2" );
m_Parser.Execute(BatchMakeScriptFile);
*/
}
i++;
}
Sub.close();
} // fin du if (sub)
else
{
std::cout << "ERROR: Unable to open file for reading." << std::endl;
}
///////////////////////////////////////////////////////////////////////////////////////////////////////Pipeline2///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
std::string nameFile2;
nameFile2=dataset;
int number_of_groups = GetNumberGroups(nameFile2);
number_of_groups = number_of_groups - 1; // First line isn't a group name
//Initialisation
char** groupIds = new char*[number_of_groups];
for(int i = 0; i < number_of_groups; ++i) groupIds[i] = NULL;
char** Groups = new char*[number_of_groups];
for(int i = 0; i < number_of_groups; ++i) Groups[i] = NULL;
char** subjgroups = new char*[number_of_groups];
for(int i = 0; i < number_of_groups; ++i) subjgroups[i] = NULL;
int L = GetGroups(nameFile2, groupIds, subjgroups, Groups);
for(int i = 0; i < L; ++i) std::cout << groupIds[i] << std::endl;
for(int i = 0; i < number_of_groups; ++i) std::cout << subjgroups[i] << std::endl;
for(int i = 0; i < number_of_groups; ++i) std::cout << Groups[i] << std::endl;
std::string final_groups;
std::string subjGroup;
for(int i = 0; i < L; ++i)
{
if (i != L-1) final_groups = final_groups + groupIds[i] + ' ';
else final_groups = final_groups + groupIds[i];
}
for(int i = 0; i < number_of_groups; ++i)
{
if (i != number_of_groups-1) subjGroup = subjGroup + subjgroups[i] +'/'+ Groups[i] + ' ';
else subjGroup = subjGroup + subjgroups[i] +'/'+ Groups[i];
}
//std::cout << final_groups << std::endl;
std::cout << subjGroup << std::endl;
//file bms
std::string BatchMakeScriptFile2 = "slicer3ThicknessSPHARM1.bms";
std::ofstream file2( BatchMakeScriptFile2.c_str());
file2 <<"set (groupIds "<< final_groups<<")"<<std::endl;
file2 <<"set (subjectsWithGroups "<< subjGroup<<")"<<std::endl;
file2 <<"set (subjWorkDir "<< subjWorkDir<<")"<<std::endl;
file2 <<"set (exprId "<< exprId<<")"<<std::endl;
file2 <<"include (/biomed-resimg/work/mjacquem/Slicer3Thickness2/SampleBatchMake/particlecorrespondance.bms)"<<std::endl;
file2.close();
/*
bm::ScriptParser m_Parser1;
m_Parser1.LoadWrappedApplication( "/biomed-resimg/work/mjacquem/Slicer3Thickness2/SampleBatchMake/bmm2" );
m_Parser1.SetBatchMakeBinaryPath( "/biomed-resimg/work/mjacquem/Slicer3Thickness2/SampleBatchMake/bmm2" );
m_Parser1.Execute(BatchMakeScriptFile2);
*/
////////////////////////////////////////////////////////////////////////////////////////////////////////Pipeline 3/////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
std::string nameFile3;
nameFile3=dataset;
std::ifstream Sub1(nameFile.c_str(),std::ios::in);
int i1=0;
if(Sub1)
{
std :: string line;
while(getline( Sub1, line ))
{
if (i1>0)
{
char labelfile[200];
char subjid[100];
char WarpedCorrespondenceMesh[200];
char CorrespondenceMesh[200];
char labelMapInput[200];
char measurementOutput[200];
char group[100];
char ThicknessSamplingResult[200];
std::string BatchMakeScriptFile = "slicer3writefile.bms";
std::ofstream file( BatchMakeScriptFile.c_str());
readFileCSV(line, group, subjid, labelMapInput, measurementOutput, labelfile, CorrespondenceMesh, WarpedCorrespondenceMesh, ThicknessSamplingResult);
file <<"set (labelMapInput "<< labelMapInput<<")"<<std::endl;
file <<"set (measurementOutput "<< measurementOutput<<")"<<std::endl;
file <<"set (spharmBinaryInput "<<labelfile<<")"<<std::endl;
file <<"set (case1 "<< subjid <<")"<<std::endl;
file <<"set (CorrespondenceMesh "<<CorrespondenceMesh<<")"<<std::endl;
file <<"set (WarpedCorrespondenceMesh "<<WarpedCorrespondenceMesh<<")"<<std::endl;
file <<"set (group "<< group <<")"<<std::endl;
file <<"set (subjWorkDir "<< subjWorkDir<<")"<<std::endl;
file <<"set (exprId "<< exprId<<")"<<std::endl;
file <<"include (/biomed-resimg/work/mjacquem/Slicer3Thickness2/SampleBatchMake/writefile.bms)"<<std::endl;
file.close();
/*
bm::ScriptParser m_Parser;
m_Parser.LoadWrappedApplication( "/biomed-resimg/work/mjacquem/Slicer3Thickness2/SampleBatchMake/bmm2" );
m_Parser.SetBatchMakeBinaryPath( "/biomed-resimg/work/mjacquem/Slicer3Thickness2/SampleBatchMake/bmm2" );
m_Parser.Execute(BatchMakeScriptFile);
*/
}
i1++;
}
Sub1.close();
} // fin du if (sub)
else
{
std::cout << "ERROR: Unable to open file for reading." << std::endl;
}
//////////////////////////////////////////////////////////////////////////////////////////////////Pipeline4////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
std::string nameFile4;
nameFile4=dataset;
//file bms
std::string BatchMakeScriptFile4 = "slicer3shapeworks.bms";
std::ofstream file4( BatchMakeScriptFile4.c_str());
file4 <<"set (groupIds "<< final_groups<<")"<<std::endl;
file4 <<"set (subjWorkDir "<< subjWorkDir<<")"<<std::endl;
file4 <<"set (exprId "<< exprId<<")"<<std::endl;
file4 <<"include (/biomed-resimg/work/mjacquem/Slicer3Thickness2/SampleBatchMake/shapeworks.bms)"<<std::endl;
file4.close();
/*
bm::ScriptParser m_Parser4;
m_Parser4.LoadWrappedApplication( "/biomed-resimg/work/mjacquem/Slicer3Thickness2/SampleBatchMake/bmm2" );
m_Parser4.SetBatchMakeBinaryPath( "/biomed-resimg/work/mjacquem/Slicer3Thickness2/SampleBatchMake/bmm2" );
m_Parser4.Execute(BatchMakeScriptFile4);
*/
////////////////////////////////////////////////////////////////////////////////////////////////Pipeline5/////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
std::string nameFile5;
nameFile5=dataset;
std::ifstream Sub2(nameFile.c_str(),std::ios::in);
int i2=0;
if(Sub2)
{
std :: string line;
while(getline( Sub2, line ))
{
if (i2>0)
{
char labelfile[200];
char subjid[100];
char WarpedCorrespondenceMesh[200];
char CorrespondenceMesh[200];
char labelMapInput[200];
char measurementOutput[200];
char group[100];
char ThicknessSamplingResult[200];
std::string BatchMakeScriptFile5 = "slicer3meshintensity.bms";
std::ofstream file( BatchMakeScriptFile5.c_str());
readFileCSV(line, group, subjid, labelMapInput, measurementOutput, labelfile, CorrespondenceMesh, WarpedCorrespondenceMesh, ThicknessSamplingResult);
file <<"set (labelMapInput "<< labelMapInput<<")"<<std::endl;
file <<"set (measurementOutput "<< measurementOutput<<")"<<std::endl;
file <<"set (spharmBinaryInput "<<labelfile<<")"<<std::endl;
file <<"set (case1 "<< subjid <<")"<<std::endl;
file <<"set (CorrespondenceMesh "<<CorrespondenceMesh<<")"<<std::endl;
file <<"set (WarpedCorrespondenceMesh "<<WarpedCorrespondenceMesh<<")"<<std::endl;
file <<"set (ThicknessSamplingResult "<<ThicknessSamplingResult<<")"<<std::endl;
file <<"set (group "<< group <<")"<<std::endl;
file <<"set (subjWorkDir "<< subjWorkDir<<")"<<std::endl;
file <<"set (exprId "<< exprId<<")"<<std::endl;
file <<"include (/biomed-resimg/work/mjacquem/Slicer3Thickness2/SampleBatchMake/meshintensity.bms)"<<std::endl;
file.close();
/*
bm::ScriptParser m_Parser;
m_Parser.LoadWrappedApplication( "/biomed-resimg/work/mjacquem/Slicer3Thickness2/SampleBatchMake/bmm2" );
m_Parser.SetBatchMakeBinaryPath( "/biomed-resimg/work/mjacquem/Slicer3Thickness2/SampleBatchMake/bmm2" );
m_Parser.Execute(BatchMakeScriptFile5);
*/
}
i2++;
}
Sub2.close();
} // fin du if (sub)
else
{
std::cout << "ERROR: Unable to open file for reading." << std::endl;
}
///////////////////////////////////////////////////////////////////////////////////////////////////////Pipeline6///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
std::string nameFile1;
nameFile1=dataset;
//file bms
std::string BatchMakeScriptFile1 = "slicer3ThicknessSPHARM2.bms";
std::ofstream file6( BatchMakeScriptFile1.c_str());
file6 <<"set (groupIds "<< final_groups<<")"<<std::endl;
file6 <<"set (subjWorkDir "<< subjWorkDir<<")"<<std::endl;
file6 <<"set (exprId "<< exprId<<")"<<std::endl;
file6 <<"set (subjectsWithGroups "<< subjGroup<<")"<<std::endl;
file6 <<"include (/biomed-resimg/work/mjacquem/Slicer3Thickness2/SampleBatchMake/correspondance.bms)"<<std::endl;
file6.close();
/*
bm::ScriptParser m_Parser2;
m_Parser2.LoadWrappedApplication( "/biomed-resimg/work/mjacquem/Slicer3Thickness2/SampleBatchMake/bmm2" );
m_Parser2.SetBatchMakeBinaryPath( "/biomed-resimg/work/mjacquem/Slicer3Thickness2/SampleBatchMake/bmm2" );
m_Parser2.Execute(BatchMakeScriptFile1);
*/
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// Memory Space liberation
for (int i = 0; i < L; ++i) delete [] groupIds[i];
delete [] groupIds;
// Memory Space liberation
for (int i = 0; i < number_of_groups; ++i) delete [] subjgroups[i];
delete [] subjgroups;
// Memory Space liberation
for (int i = 0; i < number_of_groups; ++i) delete [] Groups[i];
delete [] Groups;
return 0;
}
int main( ) {
std::string input_dir = "Input/";
// Read Nucleus File
std::string nucleus_string;
std::ifstream nucleus_file( "domgen.config" );
nucleus_file >> nucleus_string;
nucleus_file.close();
nucleus_file.clear();
// Read Configuration file
std::string config_filename = nucleus_string + ".config";
std::ifstream config_file( config_filename.c_str() );
std::string parameters_string;
int fit_ph;
double rmax;
int rpts;
int lmax;
config_file >> parameters_string >> fit_ph;
config_file >> rmax >> rpts >> lmax;
cout<<"parameters_string = "<<parameters_string<<endl;
int num_lj;
config_file >> num_lj;
config_file.close();
config_file.clear();
// Read in normalization
double calc_Z = 20;
double calc_N = 20;
//std::cout << "Enter calculated Z: " << std::endl;
//std::cin >> calc_Z;
//std::cout << "Enter calculated N: " << std::endl;
//std::cin >> calc_N;
std::string output_dir = "Output_" + parameters_string + "/Spectral_functions_kE/";
std::string parameters_filename = parameters_string + ".inp";
std::cout << "rmax = " << rmax << std::endl;
std::cout << "rpts = " << rpts << std::endl;
std::cout << "lmax = " << lmax << std::endl;
std::string n_string = "n" + nucleus_string;
std::string p_string = "p" + nucleus_string;
std::string n_filename = input_dir + n_string + ".inp";
std::string p_filename = input_dir + p_string + ".inp";
// Create Nuclear Parameter Objects
NuclearParameters Nu_n = read_nucleus_parameters( n_filename );
NuclearParameters Nu_p = read_nucleus_parameters( p_filename );
std::vector< NuclearParameters > Nu_vec;
Nu_vec.push_back( Nu_n );
Nu_vec.push_back( Nu_p );
// Read in DOM parameters
std::ifstream pfile( parameters_filename.c_str() );
if ( pfile.is_open() !=1 ) {
std::cout << "could not open file " << parameters_filename << std::endl;
std::abort();
}
pfile.close();
pfile.clear();
// Create radial grid
std::vector<double> rmesh;
std::vector<double> rweights;
double rdelt = rmax / rpts;
for( int i = 0; i < rpts; ++i ) {
rmesh.push_back( ( i + 0.5 ) * rdelt );
rweights.push_back( rdelt );
}
// Create momentum space grid for k-slice
std::vector<double> kmesh1;
double kmax1 = 6.0;
int kpts1 = 100;
double deltak1 = kmax1 / kpts1;
for ( int i = 0; i < kpts1; ++i ) {
kmesh1.push_back( ( i + 0.5 ) * deltak1 );
}
// Create momentum space grid for E-slice
std::vector<double> kmesh2; // wave number in units of fm^{-1}
std::vector<double> pmesh; // momentum in units of MeV / c
double pmin = 170;
double pmax = 650;
double deltap = 40;
int ppts = static_cast<int> ( ( pmax - pmin ) / deltap ) + 1;
for ( int i = 0; i < ppts; ++i ) {
double p = pmin + i * deltap;
pmesh.push_back( p );
double k = p / hbarc;
kmesh2.push_back( k );
}
// Prepare stuff for output files
std::vector< std::string > np_strings;
np_strings.push_back( n_string );
np_strings.push_back( p_string );
// create L and J strings for output files
std::string L_array[8] = { "s", "p", "d", "f", "g", "h", "i", "j" };
std::string J_array[8] = { "1", "3", "5", "7", "9", "11", "13", "15" };
//Potential specifications
int type = 1; // 1 is P.B. form (average), 0 is V.N. form
int mvolume = 4;
int AsyVolume = 1;
/* CALCULATIONS */
// Loop over protons and neutrons
double Zp; // number of protons in projectile
omp_set_nested(1);
#pragma omp parallel num_threads(2)
{
#pragma omp for
for ( unsigned int nu = 0; nu < Nu_vec.size(); ++nu ) {
double tz = nu - 0.5; // +0.5 for protons, -0.5 for neutrons
double calc_norm;
if ( tz < 0 ) {
Zp = 0;
calc_norm = calc_N;
}
else {
Zp = 1;
calc_norm = calc_Z;
}
// Nucleus Object
const NuclearParameters &Nu = Nu_vec[nu];
// Construct Parameters Object
Parameters p = get_parameters( parameters_filename, Nu.A, Nu.Z, Zp );
// Construct Potential Object
pot U = get_bobs_pot2( type, mvolume, AsyVolume, tz, Nu, p );
pot *U1 = &U;
// Construct Object for calculating bound-state properties
boundRspace B( rmax, rpts, Nu.Ef, Nu.ph_gap, lmax, Nu.Z, Zp, Nu.A, U1 );
// Create Energy Grid for k-slice
double Emin1 = -225;
double Emax1 = -25;
double deltaE1 = 25;
int epts1 = static_cast<int>( ( Emax1 - Emin1 ) / deltaE1 ) + 1;
std::vector<double> emesh1;
for ( int i = 0; i < epts1; ++i ) {
emesh1.push_back( Emin1 + i * deltaE1 );
}
// Create Energy grid for E-slice
double Emin2 = -300;
double Emax2 = -25;
double deltaE2 = 2;
int epts2 = static_cast<int>( ( Emax2 - Emin2 ) / deltaE2 ) + 1;
std::vector<double> emesh2;
for ( int i = 0; i < epts2; ++i ) {
emesh2.push_back( Emin2 + i * deltaE2 );
}
matrix_t S_of_kE_mtx1( kmesh1.size(), emesh1.size() );
matrix_t S_of_kE_mtx2( kmesh2.size(), emesh2.size() );
// intialize matrices to zero
for ( unsigned int i = 0; i < kmesh1.size(); ++i ) {
for ( unsigned int j = 0; j < emesh1.size(); ++j ) {
S_of_kE_mtx1( i, j ) = 0;
}
}
for ( unsigned int i = 0; i < kmesh2.size(); ++i ) {
for ( unsigned int j = 0; j < emesh2.size(); ++j ) {
S_of_kE_mtx2( i, j ) = 0;
}
}
std::vector< matrix_t > S_of_kE_mtx2_lj_vec;
// Loop over lj channels
for ( int L = 0; L < lmax + 1; ++L ) {
cout<<"l = "<<L<<endl;
for( int up = -1; up < 2; up+=2 ) {
double xj = L + up / 2.0;
int j_index = ( up - 1 ) / 2;
if ( xj < 0 ) continue;
std::string j_string;
if ( L == 0 ) j_string = J_array[ L ];
else j_string = J_array[ L + j_index ];
std::string lj_string = L_array[L] + j_string + "2";
// Create Bessel Function matrix in k and r
matrix_t bess_mtx1( kmesh1.size(), rmesh.size() );
for( unsigned int nk = 0; nk < kmesh1.size(); ++nk ) {
for( unsigned int nr = 0; nr < rmesh.size(); ++nr ) {
double rho = kmesh1[nk] * rmesh[nr];
bess_mtx1( nk, nr ) = gsl_sf_bessel_jl( L, rho );
}
}
// Create Bessel Function matrix in k and r
matrix_t bess_mtx2( kmesh2.size(), rmesh.size() );
for( unsigned int nk = 0; nk < kmesh2.size(); ++nk ) {
for( unsigned int nr = 0; nr < rmesh.size(); ++nr ) {
double rho = kmesh2[nk] * rmesh[nr];
bess_mtx2( nk, nr ) = gsl_sf_bessel_jl( L, rho );
}
}
// Calculate S( k; E ) for k-slice
for ( unsigned int m = 0; m < emesh1.size(); ++m ) {
double E = emesh1[m];
/*
std::ostringstream e_strm;
e_strm << "m" << std::abs( E );
std::string s_of_kE_lj_filename1 =
output_dir + np_strings[nu] + "_s_of_k_" +
"E_at_" + e_strm.str() + "MeV_" + L_array[L]
+ j_string + "2.out";
std::ofstream file1( s_of_kE_lj_filename1.c_str() );
*/
// Propagator
cmatrix_t G = B.propagator( rmesh, E, L, xj );
// Spectral Function in momentum space, S( k; E )
for( unsigned int nk = 0; nk < kmesh1.size(); ++nk ) {
double rsums = 0;
for( unsigned int i = 0; i < rmesh.size(); ++i ) {
double jl1 = bess_mtx1( nk, i );
for( unsigned int j = 0; j < rmesh.size(); ++j ) {
double jl2 = bess_mtx1( nk, j );
rsums -= rmesh[i] * jl1 * imag( G( i, j ) )
* rmesh[j] * jl2 * rdelt * 2 / M_PI / M_PI;
}
} // end loop over radial coordinates
// file1 << kmesh1[nk] << " " << rsums << std::endl;
S_of_kE_mtx1( nk, m ) += ( 2 * xj + 1 ) * rsums;
} // end loop over k
// file1.close();
// file1.clear();
// r-space spectral functions
} // end loop over energy
// Calculate S( k; E ) for E-slice
matrix_t S_of_kE_mtx_lj( kmesh2.size(), emesh2.size() );
for ( unsigned int m = 0; m < emesh2.size(); ++m ) {
double E = emesh2[m];
// Propagator
cmatrix_t G = B.propagator( rmesh, E, L, xj );
// Spectral Function in momentum space, S( k; E )
for( unsigned int nk = 0; nk < kmesh2.size(); ++nk ) {
double rsums = 0;
for( unsigned int i = 0; i < rmesh.size(); ++i ) {
double jl1 = bess_mtx2( nk, i );
for( unsigned int j = 0; j < rmesh.size(); ++j ) {
double jl2 = bess_mtx2( nk, j );
rsums -= rmesh[i] * jl1 * imag( G( i, j ) )
* rmesh[j] * jl2 * rdelt * 2 / M_PI / M_PI;
}
} // end loop over radial coordinates
S_of_kE_mtx_lj( nk, m ) = ( 2 * xj + 1 ) * rsums;
S_of_kE_mtx2( nk, m ) += ( 2 * xj + 1 ) * rsums;
} // end loop over k
} // end loop over energy
S_of_kE_mtx2_lj_vec.push_back( S_of_kE_mtx_lj );
}// end loop over j
} // end loop over L
// write out results summed over the lj combinations
for ( unsigned int j = 0; j < emesh1.size(); ++j ) {
std::ostringstream e_strm;
e_strm << "m" << std::abs( emesh1[j] );
std::string s_of_kE_filename1 =
output_dir + np_strings[nu] + "_s_of_k_" +
"E_at_" + e_strm.str() + "MeV.out";
std::ofstream file3( s_of_kE_filename1.c_str() );
for ( unsigned int i = 0; i < kmesh1.size(); ++i ) {
file3 << kmesh1[i] << " " << S_of_kE_mtx1( i, j ) << std::endl;
}
file3.close();
file3.clear();
}
// write in units of MeV^-4 sr^-1
double fac = std::pow( hbarc, 3 ) * 4 * M_PI;
for ( unsigned int i = 0; i < kmesh2.size(); ++i ) {
std::ostringstream k_strm;
k_strm << pmesh[i];
std::string s_of_kE_filename2 =
output_dir + np_strings[nu] + "_s_of_E_" +
"p_at_" + k_strm.str() + "MeV_over_c.out";
std::ofstream file4( s_of_kE_filename2.c_str() );
for ( unsigned int j = 0; j < emesh2.size(); ++j ) {
// write energy in terms of missing energy
// and in units of GeV
file4 << std::abs( emesh2[j]/1000) << " "
<< S_of_kE_mtx2( i, j ) / fac << " "
<< S_of_kE_mtx2( i, j ) / fac / calc_norm << std::endl;
}
file4.close();
file4.clear();
}
// write in units of MeV^-4 sr^-1
for ( unsigned int nk = 0; nk < kmesh2.size(); ++nk ) {
for ( int L = 0; L < lmax + 1; ++L ) {
std::ostringstream k_strm;
k_strm << pmesh[nk];
std::string s_of_kE_lj_filename2 =
output_dir + np_strings[nu] + "_s_of_E_p_at_"
+ k_strm.str() + "MeV_over_c_" + L_array[L]
+ ".out";
std::ofstream file2( s_of_kE_lj_filename2.c_str() );
for ( unsigned int m = 0; m < emesh2.size(); ++m ) {
// write energy in terms of missing energy
// and in units of GeV
if ( L == 0 ) {
file2 << std::abs( emesh2[m]/1000 ) << " "
<< S_of_kE_mtx2_lj_vec[0]( nk, m ) / fac
<< std::endl;
}
else {
double jg = S_of_kE_mtx2_lj_vec[2*L]( nk, m );
double jl = S_of_kE_mtx2_lj_vec[2*L- 1]( nk, m );
file2 << std::abs( emesh2[m]/1000) << " "
<< jg / fac << " " << jl / fac << " "
<< ( jg + jl ) / fac << std::endl;
}
}
file2.close();
file2.clear();
} // end loop over L
} // end loop over momentum
} // end loop over tz
} /* end of pragma loop */
return 1;
}
void overlay_plots(const string& fFile0, const string& fFile1, const string& fFile2, const string& fFile3, const string& fFile4, const string& fPlot0, const string& fPlot1, const string& fPlot2, const string& fPlot3, const string& fPlot4, const double fXmin, const double fXmax, const string& fXAxisLabel, const string& fName, const int logY, const int rescale, const double cutValue0, const double cutValue1, const string& label) {
TH1F *h[5];
TFile file0(fFile0.c_str());
h[0] = (TH1F*)file0.Get(fPlot0.c_str());
TFile file1(fFile1.c_str());
h[1] = (TH1F*)file1.Get(fPlot1.c_str());
TFile file2(fFile2.c_str());
h[2] = (TH1F*)file2.Get(fPlot2.c_str());
TFile file3(fFile3.c_str());
h[3] = (TH1F*)file3.Get(fPlot3.c_str());
TFile file4(fFile4.c_str());
h[4] = (TH1F*)file4.Get(fPlot4.c_str());
h[0]->Rebin(1);
h[1]->Rebin(1);
h[2]->Rebin(1);
h[3]->Rebin(1);
h[4]->Rebin(1);
// double ymax = (h[0]->GetMaximum()>h[1]->GetMaximum()) ? h[0]->GetMaximum() : h[1]->GetMaximum();
h[0]->GetXaxis()->SetTitle(fXAxisLabel.c_str());
h[0]->GetXaxis()->SetRangeUser(fXmin,fXmax);
// h[0]->GetYaxis()->SetRangeUser(0.5,1.25*ymax);
h[0]->SetTitleOffset(1.2,"X");
h[0]->GetXaxis()->SetTitleSize(0.04);
h[0]->GetYaxis()->SetTitleSize(0.04);
if(rescale)
{
if (h[0]->Integral()!=0)
h[0]->Scale(1/h[0]->Integral());
//----------------------------
// if (h[1]->Integral()!=0)
// h[1]->Scale(1/h[1]->Integral());
// if (h[2]->Integral()!=0)
// h[2]->Scale(1/h[2]->Integral());
//----------------------------
if (h[3]->Integral()!=0)
h[3]->Scale(1/h[3]->Integral());
if (h[4]->Integral()!=0)
h[4]->Scale(1/h[4]->Integral());
}
TCanvas *c = new TCanvas("c","",800,800);
c->cd();
c->Range(-0.4638998,-0.01028103,4.210331,0.09111118);
c->SetRightMargin(0.2286432);
h[0]->SetLineWidth(3);
// h[0]->SetLineStyle(4);
h[0]->SetLineColor(kRed);
h[0]->SetFillColor(kRed);
h[0]->SetFillStyle(3002);
// h[0]->SetMarkerSize(.6);
// h[0]->SetMarkerStyle(26);
// h[0]->SetMarkerColor(kRed);
h[0]->Draw("hist");
h[1]->SetLineWidth(3);
// h[1]->SetLineStyle(3);
h[1]->SetLineColor(kBlack);
// h[1]->SetMarkerSize(.8);
h[1]->SetMarkerStyle(20);
h[1]->SetMarkerColor(kBlack);
//----------------------------
//h[1]->Draw("sameshist");
//----------------------------
h[2]->SetLineWidth(3);
h[2]->SetLineStyle(3);
h[2]->SetLineColor(kBlack);
// h[1]->SetMarkerSize(.8);
h[2]->SetMarkerStyle(20);
h[2]->SetMarkerColor(kBlack);
//----------------------------
//h[2]->Draw("sameshist");
//----------------------------
h[3]->SetLineWidth(3);
h[3]->SetLineStyle(4);
h[3]->SetLineColor(kBlack);
// h[1]->SetMarkerSize(.8);
h[3]->SetMarkerStyle(20);
h[3]->SetMarkerColor(kBlack);
h[3]->Draw("sameshist");
h[4]->SetLineWidth(3);
h[4]->SetLineStyle(5);
h[4]->SetLineColor(kBlack);
// h[1]->SetMarkerSize(.8);
h[4]->SetMarkerStyle(20);
h[4]->SetMarkerColor(kBlack);
h[4]->Draw("sameshist");
double maximum = 0;
if( h[0]->GetMaximum() > maximum )
maximum = h[0]->GetMaximum() ;
//-------------------------------
// if( h[1]->GetMaximum() > maximum )
// maximum = h[1]->GetMaximum();
// if( h[2]->GetMaximum() > maximum )
// maximum = h[2]->GetMaximum();
//-------------------------------
if( h[3]->GetMaximum() > maximum )
maximum = h[3]->GetMaximum();
if( h[4]->GetMaximum() > maximum )
maximum = h[4]->GetMaximum();
h[0]->GetYaxis()->SetRangeUser(0,maximum+maximum*0.1);
//update the current pad, needed to modify statboxes
gPad->Update();
// get the statboxes and set color
TPaveStats *st1 = (TPaveStats*)h[0]->GetListOfFunctions()->FindObject("stats");
st1->SetTextColor(kRed);
st1->SetLineColor(kRed);
st1->SetOptStat(1111111);
//------------------------------
// TPaveStats *st2 = (TPaveStats*)h[1]->GetListOfFunctions()->FindObject("stats");
// st2->SetTextColor(kBlack);
// st2->SetLineColor(kBlack);
// st2->SetOptStat(1111111);
// TPaveStats *st3 = (TPaveStats*)h[2]->GetListOfFunctions()->FindObject("stats");
// st3->SetTextColor(kBlack);
// st3->SetLineColor(kBlack);
// st3->SetOptStat(1111111);
//------------------------------
TPaveStats *st4 = (TPaveStats*)h[3]->GetListOfFunctions()->FindObject("stats");
st4->SetTextColor(kBlack);
st4->SetLineColor(kBlack);
st4->SetOptStat(1111111);
TPaveStats *st5 = (TPaveStats*)h[4]->GetListOfFunctions()->FindObject("stats");
st5->SetTextColor(kBlack);
st5->SetLineColor(kBlack);
st5->SetOptStat(1111111);
// set the position of the statboxes
double x1 = st1->GetX1NDC();
double y1 = st1->GetY1NDC();
double x2 = st1->GetX2NDC();
double y2 = st1->GetY2NDC();
//double xx = x2-x1;
double yy = y2-y1;
//--------------------------
// st2->SetX1NDC(x1);
// st2->SetY1NDC(y1-yy);
// st2->SetX2NDC(x2);
// st2->SetY2NDC(y1);
// st3->SetX1NDC(x1);
// st3->SetY1NDC(y1-yy-yy);
// st3->SetX2NDC(x2);
// st3->SetY2NDC(y1-yy);
//--------------------------
st4->SetX1NDC(x1);
st4->SetY1NDC(y1-yy-yy-yy);
st4->SetX2NDC(x2);
st4->SetY2NDC(y1-yy-yy);
st5->SetX1NDC(x1);
st5->SetY1NDC(y1-yy-yy-yy-yy);
st5->SetX2NDC(x2);
st5->SetY2NDC(y1-yy-yy-yy);
gPad->Modified();
TLegend *legend = new TLegend(.4,.91,.75,.99);
legend->SetBorderSize(1);
legend->SetFillColor(0);
// legend->SetFillStyle(0);
legend->AddEntry(h[0],"SM background","l");
//--------------------------
// legend->AddEntry(h[1],"Axigluon + W , M = 150 GeV","l");
// legend->AddEntry(h[2],"Axigluon + W , M = 500 GeV","l");
//--------------------------
legend->AddEntry(h[3],"Axigluon + W , M = 1000 GeV","l");
legend->AddEntry(h[4],"Axigluon + W , M = 1500 GeV","l");
legend->Draw();
// TLine line0(cutValue0,0,cutValue0,h[1]->GetMaximum());
// line0.SetLineColor(kRed);
// line0.Draw("same");
// TLine line1(cutValue1,0,cutValue1,h[1]->GetMaximum());
// line1.SetLineColor(kRed);
// line1.Draw("same");
TLatex l;
l.SetTextAlign(12);
l.SetTextSize(0.04);
l.SetTextFont(62);
l.SetNDC();
l.DrawLatex(0.6,0.8,label.c_str());
if(logY==1)
c->SetLogy();
string fileName = fName;
c->SaveAs(fileName.c_str());
delete legend;
delete c;
}
