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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.
//g++ -O3 main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp -s -o dcm2niix -lz
//if you do not have zlib,you can compile without it
// g++ -O3 -DmyDisableZLib main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp -s -o dcm2niix
//or you can build your own copy:
// to compile you will first want to build the Z library, then compile the project
// cd zlib-1.2.8
// sudo ./configure;
// sudo make
//to generate combined 32-bit and 64-bit builds for OSX :
// g++ -O3 -x c++ main_console.c nii_dicom.c nifti1_io_core.c nii_ortho.c nii_dicom_batch.c -s -arch x86_64 -o dcm2niix64 -lz
// g++ -O3 -x c++ main_console.c nii_dicom.c nifti1_io_core.c nii_ortho.c nii_dicom_batch.c -s -arch i386 -o dcm2niix32 -lz
// lipo -create dcm2niix32 dcm2niix64 -o dcm2niix
//On windows with mingw you may get "fatal error: zlib.h: No such file
// to remedy, run "mingw-get install libz-dev" from mingw
//Alternatively, windows users with VisualStudio can compile this project
// vcvarsall amd64
// cl /EHsc main_console.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp -DmyDisableOpenJPEG -DmyDisableJasper /odcm2niix
//#define mydebugtest //automatically process directory specified in main, ignore input arguments
#include <stdlib.h>
#include <sys/stat.h>
#include <stdbool.h>
#include <ctype.h>
#include <string.h>
#include <stddef.h>
#include <float.h>
//#include <unistd.h>
#include <time.h> // clock_t, clock, CLOCKS_PER_SEC
#include <stdio.h>
#include "nii_dicom_batch.h"
#include "nii_dicom.h"
#include "nifti1_io_core.h"
#include <math.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()
void showHelp(const char * argv[], struct TDCMopts opts) {
const char *cstr = removePath(argv[0]);
printf("usage: %s [options] <in_folder>\n", cstr);
printf(" Options :\n");
printf(" -b : BIDS sidecar (y/n, default n)\n");
#ifdef mySegmentByAcq
printf(" -f : filename (%%a=antenna (coil) number, %%c=comments, %%d=description, %%e echo number, %%f=folder name, %%i ID of patient, %%m=manufacturer, %%n=name of patient, %%p=protocol, %%q=sequence number, %%s=series number, %%t=time, %%u=acquisition number, %%z sequence name; default '%s')\n",opts.filename);
#else
printf(" -f : filename (%%a=antenna (coil) number, %%c=comments, %%d=description, %%e echo number, %%f=folder name, %%i ID of patient, %%m=manufacturer, %%n=name of patient, %%p=protocol, %%s=series number, %%t=time, %%u=acquisition number, %%z sequence name; default '%s')\n",opts.filename);
#endif
printf(" -h : show help\n");
printf(" -m : merge 2D slices from same series regardless of study time, echo, coil, orientation, etc. (y/n, default n)\n");
printf(" -o : output directory (omit to save to input folder)\n");
printf(" -s : single file mode, do not convert other images in folder (y/n, default n)\n");
printf(" -t : text notes includes private patient details (y/n, default n)\n");
printf(" -v : verbose (y/n, default n)\n");
printf(" -x : crop (y/n, default n)\n");
char gzCh = 'n';
if (opts.isGz) gzCh = 'y';
#ifdef myDisableZLib
if (strlen(opts.pigzname) > 0)
printf(" -z : gz compress images (y/n, default %c)\n", gzCh);
else
printf(" -z : gz compress images (y/n, default %c) [REQUIRES pigz]\n", gzCh);
#else
printf(" -z : gz compress images (y/i/n, default %c) [y=pigz, i=internal, n=no]\n", gzCh);
#endif
#if defined(_WIN64) || defined(_WIN32)
printf(" Defaults stored in Windows registry\n");
printf(" Examples :\n");
printf(" %s c:\\DICOM\\dir\n", cstr);
printf(" %s -o c:\\out\\dir c:\\DICOM\\dir\n", cstr);
printf(" %s -f mystudy%%s c:\\DICOM\\dir\n", cstr);
printf(" %s -o \"c:\\dir with spaces\\dir\" c:\\dicomdir\n", cstr);
#else
printf(" Defaults file : %s\n", opts.optsname);
printf(" Examples :\n");
printf(" %s /Users/chris/dir\n", cstr);
printf(" %s -o /users/cr/outdir/ -z y ~/dicomdir\n", cstr);
printf(" %s -f mystudy%%s ~/dicomdir\n", cstr);
printf(" %s -o \"~/dir with spaces/dir\" ~/dicomdir\n", cstr);
#endif
} //showHelp()
//#define mydebugtest
int main(int argc, const char * argv[])
{
struct TDCMopts opts;
readIniFile(&opts, argv); //set default preferences
#ifdef mydebugtest
//strcpy(opts.indir, "/Users/rorden/desktop/sliceOrder/dicom2/Philips_PARREC_Rotation/NoRotation/DBIEX_4_1.PAR");
//strcpy(opts.indir, "/Users/rorden/desktop/sliceOrder/dicom2/test");
strcpy(opts.indir, "e:\\t1s");
#else
#if defined(__APPLE__)
#define kOS "MacOS"
#elif (defined(__linux) || defined(__linux__))
#define kOS "Linux"
#else
#define kOS "Windows"
#endif
printf("Chris Rorden's dcm2niiX version %s (%llu-bit %s)\n",kDCMvers, (unsigned long long) sizeof(size_t)*8, kOS);
if (argc < 2) {
showHelp(argv, opts);
return 0;
}
bool isCustomOutDir = false;
int i = 1;
int lastCommandArg = 0;
while (i < (argc)) { //-1 as final parameter is DICOM directory
if ((strlen(argv[i]) > 1) && (argv[i][0] == '-')) { //command
if (argv[i][1] == 'h')
showHelp(argv, opts);
else if ((argv[i][1] == 'b') && ((i+1) < argc)) {
i++;
if ((argv[i][0] == 'n') || (argv[i][0] == 'N') || (argv[i][0] == '0'))
opts.isCreateBIDS = false;
else
opts.isCreateBIDS = true;
} else if ((argv[i][1] == 'm') && ((i+1) < argc)) {
i++;
if ((argv[i][0] == 'n') || (argv[i][0] == 'N') || (argv[i][0] == '0'))
opts.isForceStackSameSeries = false;
else
opts.isForceStackSameSeries = true;
} else if ((argv[i][1] == 's') && ((i+1) < argc)) {
i++;
if ((argv[i][0] == 'n') || (argv[i][0] == 'N') || (argv[i][0] == '0'))
opts.isOnlySingleFile = false;
else
opts.isOnlySingleFile = true;
} else if ((argv[i][1] == 't') && ((i+1) < argc)) {
i++;
if ((argv[i][0] == 'n') || (argv[i][0] == 'N') || (argv[i][0] == '0'))
opts.isCreateText = false;
else
opts.isCreateText = true;
} else if ((argv[i][1] == 'v') && ((i+1) < argc)) {
i++;
if ((argv[i][0] == 'n') || (argv[i][0] == 'N') || (argv[i][0] == '0')) //0: verbose OFF
opts.isVerbose = 0;
else if ((argv[i][0] == 'h') || (argv[i][0] == 'H') || (argv[i][0] == '2')) //2: verbose HYPER
opts.isVerbose = 2;
else
opts.isVerbose = 1; //1: verbose ON
} else if ((argv[i][1] == 'x') && ((i+1) < argc)) {
i++;
if ((argv[i][0] == 'n') || (argv[i][0] == 'N') || (argv[i][0] == '0'))
opts.isCrop = false;
else
opts.isCrop = true;
} else if ((argv[i][1] == 'z') && ((i+1) < argc)) {
i++;
if ((argv[i][0] == 'i') || (argv[i][0] == 'I') ) {
opts.isGz = true; //force use of internal compression instead of pigz
strcpy(opts.pigzname,"");
} else if ((argv[i][0] == 'n') || (argv[i][0] == 'N') || (argv[i][0] == '0'))
opts.isGz = false;
else
opts.isGz = true;
} else if ((argv[i][1] == 'f') && ((i+1) < argc)) {
i++;
strcpy(opts.filename,argv[i]);
} else if ((argv[i][1] == 'o') && ((i+1) < argc)) {
i++;
isCustomOutDir = true;
strcpy(opts.outdir,argv[i]);
}
lastCommandArg = i;
} //if parameter is a command
i ++; //read next parameter
} //while parameters to read
//printf("%d %d",argc,lastCommandArg);
if (argc == (lastCommandArg+1)) { //+1 as array indexed from 0
//the user did not provide an input filename, report filename structure
char niiFilename[1024];
strcpy(opts.outdir,"");//no input supplied
nii_createDummyFilename(niiFilename, opts);
printf("%s\n",niiFilename);
return EXIT_SUCCESS;
}
#endif
clock_t start = clock();
for (i = (lastCommandArg+1); i < argc; i++) {
strcpy(opts.indir,argv[i]); // [argc-1]
if (!isCustomOutDir) strcpy(opts.outdir,opts.indir);
if (nii_loadDir(&opts) != EXIT_SUCCESS)
return EXIT_FAILURE;
}
printf ("Conversion required %f seconds.\n",((float)(clock()-start))/CLOCKS_PER_SEC);
saveIniFile(opts);
return EXIT_SUCCESS;
}
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