static void SetUpTestCase(void)
{
Sub1();
++x;
}
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;
}
IUTEST(Foo, Test1)
{
Sub1();
++x;
}
