bool load_4d_nii(const char* file_name,boost::ptr_vector<DwiHeader>& dwi_files)
{
gz_nifti analyze_header;
if(!analyze_header.load_from_file(file_name))
return false;
std::cout << "loading 4d nifti" << std::endl;
std::vector<double> bvals,bvecs;
{
QString bval_name,bvec_name;
bval_name = QFileInfo(file_name).absolutePath() + "/bvals";
if(!QFileInfo(bval_name).exists())
bval_name = QFileInfo(file_name).absolutePath() + "/bvals.txt";
bvec_name = QFileInfo(file_name).absolutePath() + "/bvecs";
if(!QFileInfo(bvec_name).exists())
bvec_name = QFileInfo(file_name).absolutePath() + "/bvecs.txt";
if(QFileInfo(bval_name).exists() && QFileInfo(bvec_name).exists())
{
load_bval(bval_name.toLocal8Bit().begin(),bvals);
load_bvec(bvec_name.toLocal8Bit().begin(),bvecs);
if(analyze_header.dim(4) != bvals.size() ||
bvals.size()*3 != bvecs.size())
{
bvals.clear();
bvecs.clear();
}
else
std::cout << "bvals and bvecs loaded" << std::endl;
}
}
image::basic_image<float,4> grad_dev;
image::basic_image<unsigned char,3> mask;
if(QFileInfo(QFileInfo(file_name).absolutePath() + "/grad_dev.nii.gz").exists())
{
gz_nifti grad_header;
if(grad_header.load_from_file(QString(QFileInfo(file_name).absolutePath() + "/grad_dev.nii.gz").toLocal8Bit().begin()))
{
grad_header.toLPS(grad_dev);
std::cout << "grad_dev used" << std::endl;
}
}
if(QFileInfo(QFileInfo(file_name).absolutePath() + "/nodif_brain_mask.nii.gz").exists())
{
gz_nifti mask_header;
if(mask_header.load_from_file(QString(QFileInfo(file_name).absolutePath() + "/nodif_brain_mask.nii.gz").toLocal8Bit().begin()))
{
mask_header.toLPS(mask);
std::cout << "mask used" << std::endl;
}
}
{
float vs[4];
analyze_header.get_voxel_size(vs);
for(unsigned int index = 0;check_prog(index,analyze_header.dim(4));++index)
{
std::auto_ptr<DwiHeader> new_file(new DwiHeader);
if(!analyze_header.toLPS(new_file->image,false))
break;
image::lower_threshold(new_file->image,0);
new_file->file_name = file_name;
std::ostringstream out;
out << index;
new_file->file_name += out.str();
std::copy(vs,vs+3,new_file->voxel_size);
if(!bvals.empty())
{
new_file->bvalue = bvals[index];
new_file->bvec[0] = bvecs[index*3];
new_file->bvec[1] = bvecs[index*3+1];
new_file->bvec[2] = bvecs[index*3+2];
new_file->bvec.normalize();
if(new_file->bvalue < 10)
{
new_file->bvalue = 0;
new_file->bvec = image::vector<3>(0,0,0);
}
}
if(index == 0 && !grad_dev.empty())
new_file->grad_dev.swap(grad_dev);
if(index == 0 && !mask.empty())
new_file->mask.swap(mask);
dwi_files.push_back(new_file.release());
}
}
return true;
}
int src(int ac, char *av[])
{
po::options_description rec_desc("dicom parsing options");
rec_desc.add_options()
("help", "help message")
("action", po::value<std::string>(), "src:dicom parsing")
("source", po::value<std::string>(), "assign the directory for the dicom files")
("recursive", po::value<std::string>(), "search subdirectories")
("b_table", po::value<std::string>(), "assign the b-table")
("bval", po::value<std::string>(), "assign the b value")
("bvec", po::value<std::string>(), "assign the b vector")
("output", po::value<std::string>(), "assign the output filename")
;
if(!ac)
{
std::cout << rec_desc << std::endl;
return 1;
}
po::variables_map vm;
po::store(po::command_line_parser(ac, av).options(rec_desc).run(), vm);
po::notify(vm);
std::string source = vm["source"].as<std::string>();
std::string ext;
if(source.size() > 4)
ext = std::string(source.end()-4,source.end());
boost::ptr_vector<DwiHeader> dwi_files;
QStringList file_list;
if(ext ==".nii" || ext == ".dcm" || ext == "dseq" || ext == "i.gz")
{
std::cout << "image=" << source.c_str() << std::endl;
file_list << source.c_str();
}
else
{
std::cout << "load files in directory " << source.c_str() << std::endl;
QDir directory = QString(source.c_str());
if(vm.count("recursive"))
{
std::cout << "search recursively in the subdir" << std::endl;
file_list = search_files(source.c_str(),"*.dcm");
}
else
{
file_list = directory.entryList(QStringList("*.dcm"),QDir::Files|QDir::NoSymLinks);
if(file_list.empty())
file_list = directory.entryList(QStringList("*.nii.gz"),QDir::Files|QDir::NoSymLinks);
for (unsigned int index = 0;index < file_list.size();++index)
file_list[index] = QString(source.c_str()) + "/" + file_list[index];
}
std::cout << "A total of " << file_list.size() <<" files found in the directory" << std::endl;
}
if(file_list.empty())
{
std::cout << "No file found for creating src" << std::endl;
return -1;
}
if(!load_all_files(file_list,dwi_files))
{
std::cout << "Invalid file format" << std::endl;
return -1;
}
if(vm.count("b_table"))
{
std::string table_file_name = vm["b_table"].as<std::string>();
std::ifstream in(table_file_name.c_str());
if(!in)
{
std::cout << "Failed to open b-table" <<std::endl;
return -1;
}
std::string line;
std::vector<double> b_table;
while(std::getline(in,line))
{
std::istringstream read_line(line);
std::copy(std::istream_iterator<double>(read_line),
std::istream_iterator<double>(),
std::back_inserter(b_table));
}
if(b_table.size() != dwi_files.size()*4)
{
std::cout << "Mismatch between b-table and the loaded images" << std::endl;
return -1;
}
for(unsigned int index = 0,b_index = 0;index < dwi_files.size();++index,b_index += 4)
{
dwi_files[index].set_bvalue(b_table[b_index]);
dwi_files[index].set_bvec(b_table[b_index+1],b_table[b_index+2],b_table[b_index+3]);
}
std::cout << "B-table " << table_file_name << " loaded" << std::endl;
}
if(vm.count("bval") && vm.count("bvec"))
{
std::vector<double> bval,bvec;
std::cout << "load bval=" << vm["bval"].as<std::string>() << std::endl;
std::cout << "load bvec=" << vm["bvec"].as<std::string>() << std::endl;
load_bval(vm["bval"].as<std::string>().c_str(),bval);
load_bvec(vm["bvec"].as<std::string>().c_str(),bvec);
if(bval.size() != dwi_files.size())
{
std::cout << "Mismatch between bval file and the loaded images" << std::endl;
return -1;
}
if(bvec.size() != dwi_files.size()*3)
{
std::cout << "Mismatch between bvec file and the loaded images" << std::endl;
return -1;
}
for(unsigned int index = 0;index < dwi_files.size();++index)
{
dwi_files[index].set_bvalue(bval[index]);
dwi_files[index].set_bvec(bvec[index*3],bvec[index*3+1],bvec[index*3+2]);
}
}
if(dwi_files.empty())
{
std::cout << "No file readed. Abort." << std::endl;
return 1;
}
double max_b = 0;
for(unsigned int index = 0;index < dwi_files.size();++index)
{
if(dwi_files[index].get_bvalue() < 100)
dwi_files[index].set_bvalue(0);
max_b = std::max(max_b,(double)dwi_files[index].get_bvalue());
}
if(max_b == 0.0)
{
std::cout << "Cannot find b-table from the header. You may need to load an external b-table using--b_table or --bval and --bvec." << std::endl;
return 1;
}
std::cout << "Output src " << vm["output"].as<std::string>().c_str() << std::endl;
DwiHeader::output_src(vm["output"].as<std::string>().c_str(),dwi_files,0);
return 0;
}
int src(void)
{
std::string source = po.get("source");
std::string ext;
if(source.size() > 4)
ext = std::string(source.end()-4,source.end());
std::string output;
if(po.has("output"))
output = po.get("output");
if(QFileInfo(output.c_str()).exists())
{
std::cout << output << " exists. skipping..." << std::endl;
return 1;
}
std::vector<std::shared_ptr<DwiHeader> > dwi_files;
QStringList file_list;
if(ext ==".nii" || ext == ".dcm" || ext == "dseq" || ext == "i.gz")
{
std::cout << "image=" << source.c_str() << std::endl;
std::istringstream ss(source);
std::string token;
while(std::getline(ss, token, ','))
file_list << source.c_str();
if(!po.has("output"))
output = file_list.front().toStdString() + ".src.gz";
}
else
{
std::cout << "load files in directory " << source.c_str() << std::endl;
QDir directory = QString(source.c_str());
if(po.has("recursive"))
{
std::cout << "search recursively in the subdir" << std::endl;
file_list = search_files(source.c_str(),"*.dcm");
}
else
{
file_list = directory.entryList(QStringList("*.dcm"),QDir::Files|QDir::NoSymLinks);
if(file_list.empty())
file_list = directory.entryList(QStringList("*.nii.gz"),QDir::Files|QDir::NoSymLinks);
if(file_list.empty())
file_list = directory.entryList(QStringList("*.fdf"),QDir::Files|QDir::NoSymLinks);
for (unsigned int index = 0;index < file_list.size();++index)
file_list[index] = QString(source.c_str()) + "/" + file_list[index];
}
std::cout << "A total of " << file_list.size() <<" files found in the directory" << std::endl;
if(!po.has("output"))
output = source + ".src.gz";
}
if(file_list.empty())
{
std::cout << "No file found for creating src" << std::endl;
return 1;
}
if(!load_all_files(file_list,dwi_files))
{
std::cout << "Invalid file format" << std::endl;
return 1;
}
if(po.has("b_table"))
{
std::string table_file_name = po.get("b_table");
std::ifstream in(table_file_name.c_str());
if(!in)
{
std::cout << "Failed to open b-table" <<std::endl;
return 1;
}
std::string line;
std::vector<double> b_table;
while(std::getline(in,line))
{
std::istringstream read_line(line);
std::copy(std::istream_iterator<double>(read_line),
std::istream_iterator<double>(),
std::back_inserter(b_table));
}
if(b_table.size() != dwi_files.size()*4)
{
std::cout << "Mismatch between b-table and the loaded images" << std::endl;
return 1;
}
for(unsigned int index = 0,b_index = 0;index < dwi_files.size();++index,b_index += 4)
{
dwi_files[index]->set_bvalue(b_table[b_index]);
dwi_files[index]->set_bvec(b_table[b_index+1],b_table[b_index+2],b_table[b_index+3]);
}
std::cout << "B-table " << table_file_name << " loaded" << std::endl;
}
if(po.has("bval") && po.has("bvec"))
{
std::vector<double> bval,bvec;
std::cout << "load bval=" << po.get("bval") << std::endl;
std::cout << "load bvec=" << po.get("bvec") << std::endl;
load_bval(po.get("bval").c_str(),bval);
load_bvec(po.get("bvec").c_str(),bvec);
if(bval.size() != dwi_files.size())
{
std::cout << "Mismatch between bval file and the loaded images" << std::endl;
return 1;
}
if(bvec.size() != dwi_files.size()*3)
{
std::cout << "Mismatch between bvec file and the loaded images" << std::endl;
return 1;
}
for(unsigned int index = 0;index < dwi_files.size();++index)
{
dwi_files[index]->set_bvalue(bval[index]);
dwi_files[index]->set_bvec(bvec[index*3],bvec[index*3+1],bvec[index*3+2]);
}
}
if(dwi_files.empty())
{
std::cout << "No file readed. Abort." << std::endl;
return 1;
}
double max_b = 0;
for(unsigned int index = 0;index < dwi_files.size();++index)
{
if(dwi_files[index]->get_bvalue() < 100)
dwi_files[index]->set_bvalue(0);
max_b = std::max(max_b,(double)dwi_files[index]->get_bvalue());
}
if(max_b == 0.0)
{
std::cout << "Cannot find b-table from the header. You may need to load an external b-table using--b_table or --bval and --bvec." << std::endl;
return 1;
}
std::cout << "Output src to " << output << std::endl;
DwiHeader::output_src(output.c_str(),dwi_files,
po.get<int>("up_sampling",0),
po.get<int>("sort_b_table",0));
return 0;
}
