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// main.m dcm2niix
// by Chris Rorden on 3/22/14, see license.txt
// Copyright (c) 2014 Chris Rorden. All rights reserved.
// yaml batch suport by Benjamin Irving, 2016 - maintains copyright
#include <stdlib.h>
#include <stdbool.h>
#include <time.h> // clock_t, clock, CLOCKS_PER_SEC
#include <stdio.h>
#include <cmath>
#include <string>
#include <iostream>
#include "nii_dicom_batch.h"
#include <fstream>
#include <yaml-cpp/yaml.h>
const char* removePath(const char* path) { // "/usr/path/filename.exe" -> "filename.exe"
const char* pDelimeter = strrchr (path, '\\');
if (pDelimeter)
path = pDelimeter+1;
pDelimeter = strrchr (path, '/');
if (pDelimeter)
path = pDelimeter+1;
return path;
} //removePath()
int rmainbatch(TDCMopts opts)
{
printf("Chris Rorden's dcm2niiX version %s (%lu-bit)\n",kDCMvers, sizeof(size_t)*8);
clock_t start = clock();
nii_loadDir(&opts);
printf ("Conversion required %f seconds.\n",((float)(clock()-start))/CLOCKS_PER_SEC);
return EXIT_SUCCESS;
}
int main(int argc, const char * argv[])
{
if (argc != 2) {
std::cout << "Do not include additional inputs with a config file \n";
throw;
}
// Process it all via a yaml file
std::string yaml_file = argv[1];
std::cout << "yaml_path: " << yaml_file << std::endl;
YAML::Node config = YAML::LoadFile(yaml_file);
struct TDCMopts opts;
readIniFile(&opts, argv); //setup defaults, e.g. path to pigz
opts.isCreateBIDS = config["Options"]["isCreateBIDS"].as<bool>();
opts.isOnlySingleFile = config["Options"]["isOnlySingleFile"].as<bool>();
opts.isCreateText = false;
opts.isVerbose = 0;
opts.isGz = config["Options"]["isGz"].as<bool>(); //save data as compressed (.nii.gz) or raw (.nii)
/*bool isInternalGz = config["Options"]["isInternalGz"].as<bool>();
if (isInternalGz) {
strcpy(opts.pigzname, "”); //do NOT use pigz: force internal compressor
//in general, pigz is faster unless you have a very slow network, in which case the internal compressor is better
}*/
for (auto i: config["Files"]) {
std::string indir = i["in_dir"].as<std::string>();
strcpy(opts.indir, indir.c_str());
std::string outdir = i["out_dir"].as<std::string>();
strcpy(opts.outdir, outdir.c_str());
std::string filename = i["filename"].as<std::string>();
strcpy(opts.filename, filename.c_str());
rmainbatch(opts);
}
return 1;
}
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