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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 support by Benjamin Irving, 2016 - maintains copyright
#include <stdbool.h> //requires VS 2015 or later
#ifdef _MSC_VER
#include <io.h> //access()
#ifndef F_OK
#define F_OK 0 /* existence check */
#endif
#else
#include <unistd.h> //access()
#endif
#include "nii_dicom.h"
#include "nii_dicom_batch.h"
#include <cmath>
#include <fstream>
#include <iostream>
#include <stdio.h>
#include <stdlib.h>
#include <string>
#include <time.h> // clock_t, clock, CLOCKS_PER_SEC
#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) {
clock_t start = clock();
nii_loadDir(&opts);
printf("Conversion required %f seconds.\n", ((float)(clock() - start)) / CLOCKS_PER_SEC);
return EXIT_SUCCESS;
} // rmainbatch()
void showHelp(const char *argv[]) {
const char *cstr = removePath(argv[0]);
printf("Usage: %s <batch_config.yml>\n", cstr);
printf("\n");
printf("The configuration file must be in yaml format as shown below\n");
printf("\n");
printf("### START YAML FILE ###\n");
printf("Options:\n");
printf(" isGz: false\n");
printf(" isFlipY: false\n");
printf(" isVerbose: false\n");
printf(" isCreateBIDS: false\n");
printf(" isOnlySingleFile: false\n");
printf("Files:\n");
printf(" -\n");
printf(" in_dir: /path/to/first/folder\n");
printf(" out_dir: /path/to/output/folder\n");
printf(" filename: dcemri\n");
printf(" -\n");
printf(" in_dir: /path/to/second/folder\n");
printf(" out_dir: /path/to/output/folder\n");
printf(" filename: fa3\n");
printf("### END YAML FILE ###\n");
printf("\n");
#if defined(_WIN64) || defined(_WIN32)
printf(" Example :\n");
printf(" %s c:\\dir\\yaml.yml\n", cstr);
printf(" %s \"c:\\dir with spaces\\yaml.yml\"\n", cstr);
#else
printf(" Examples :\n");
printf(" %s /Users/chris/yaml.yml\n", cstr);
printf(" %s \"/Users/dir with spaces/yaml.yml\"\n", cstr);
#endif
} // showHelp()
int main(int argc, const char *argv[]) {
#if defined(__APPLE__)
#define kOS "MacOS"
#elif (defined(__linux) || defined(__linux__))
#define kOS "Linux"
#else
#define kOS "Windows"
#endif
printf("dcm2niibatch using Chris Rorden's dcm2niiX version %s (%llu-bit %s)\n", kDCMvers, (unsigned long long)sizeof(size_t) * 8, kOS);
if (argc != 2) {
if (argc < 2)
printf(" Please provide location of config file\n");
else
printf(" Do not include additional inputs with a config file\n");
printf("\n");
showHelp(argv);
return EXIT_FAILURE;
}
if (access(argv[1], F_OK) == -1) {
printf(" Please provide location of config file\n");
printf("\n");
showHelp(argv);
return EXIT_FAILURE;
}
// 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.isFlipY = config["Options"]["isFlipY"].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 EXIT_SUCCESS;
} // main()
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