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Slicer3ThicknessSpharm.cpp
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Slicer3ThicknessSpharm.cpp
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# include <iostream>
#include <unistd.h>
#include "Slicer3ThicknessSpharmCLP.h"
#include "string"
#include <vector>
#include "errno.h"
#include <fstream>
#include "bmScriptParser.h"
void readFileCSV(std::string line, char group[100], char subjid[100], char labelMapInput[200], char measurementOutput[200], char labelfile[100],char CorrespondenceMesh[200],char WarpedCorrespondenceMesh[200],char ThicknessSamplingResult[200])
{
int pos1=0, pos2=0, pos3=0,pos4=0, pos5=0, pos6=0, pos7=0, pos8=0, l=0;
pos1 = line.find(' ',0);
l = line.copy(group,pos1,0);
group[l] = '\0';
pos2 = line.find(' ',pos1+1);
l = line.copy(subjid,pos2-pos1-1,pos1+1);
subjid[l] = '\0';
pos3 = line.find(' ',pos2+1);
l = line.copy(labelMapInput,pos3-pos2-1,pos2+1);
labelMapInput[l] = '\0';
pos4 = line.find(' ',pos3+1);
l = line.copy(measurementOutput,pos4-pos3-1,pos3+1);
measurementOutput[l] = '\0';
pos5 = line.find(' ',pos4+1);
l = line.copy(labelfile,pos5-pos4-1,pos4+1);
labelfile[l] = '\0';
pos6 = line.find(' ',pos5+1);
l = line.copy(CorrespondenceMesh,pos6-pos5-1,pos5+1);
CorrespondenceMesh[l] = '\0';
pos7 = line.find(' ',pos6+1);
l = line.copy(WarpedCorrespondenceMesh,pos7-pos6-1,pos6+1);
WarpedCorrespondenceMesh[l] = '\0';
pos8=line.find(' ',pos7+1);
l = line.copy(ThicknessSamplingResult,pos8-pos7-1,pos7+1);
ThicknessSamplingResult[l] = '\0';
}
int GetNumberGroups(std::string file)
{
std::ifstream groups(file.c_str(), std::ios::in);
int c = 0;
if (groups)
{
std::string s;
while ( getline(groups,s) ) c++;
groups.close();
}
else std::cerr << "File doesn't exist" << std::endl;
return c;
}
int GetGroups(std::string file, char** groupIds , char** subjgroups, char** Groups)
{
std::ifstream groups(file.c_str(), std::ios::in);
int length = 0;
int length1 = 0;
int length2 = 0;
int first_line = 0;
if (groups)
{
std::string s;
while ( getline(groups,s) )
{
if (first_line != 0)
{
// Get the values
int pos = s.find(' ',0);
int l;
char group_name[20]; l = s.copy(group_name,pos,0); group_name[l] = '\0';
int pos1= s.find(' ',pos+1);
int t;
char subj_name[100]; t =s.copy(subj_name,pos1-pos-1,pos+1); subj_name[t]='\0';
int test = 0;
for (int i = 0; i < length; ++i) if ( strcmp(groupIds[i], group_name) == 0 ) test = 1;
//New entry if test = 0
if (test == 0)
{
groupIds[length] = new char[pos+1];
strcpy(groupIds[length],group_name);
length++;
}
subjgroups[length1]= new char[pos1-pos+1];
strcpy(subjgroups[length1],subj_name);
length1++;
Groups[length2] = new char[pos+1];
strcpy(Groups[length2],group_name);
length2++;
}
first_line = 1;
s.clear();
}
groups.close();
}
else std::cerr << "File doesn't exist" << std::endl;
return length;
}
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;
}