File size: 5,744 Bytes
4559903 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 | #include <QDir>
#include <iostream>
#include <iterator>
#include <string>
#include "image/image.hpp"
#include "boost/program_options.hpp"
#include "dicom/dwi_header.hpp"
namespace po = boost::program_options;
QStringList search_files(QString dir,QString filter);
void load_bval(const char* file_name,std::vector<double>& bval);
void load_bvec(const char* file_name,std::vector<double>& b_table);
bool load_all_files(QStringList file_list,boost::ptr_vector<DwiHeader>& dwi_files);
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;
}
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