int main(const int argc, const char *argv[]) {
int nextarg;
NaClLogModuleInit();
NaClLogSetVerbosity(LOG_FATAL);
if (0 != setvbuf(stdout, g_standard_output_buffer, _IOLBF,
sizeof g_standard_output_buffer)) {
NaClLog(LOG_FATAL, "vdiff: setvbuf failed\n");
}
#if NACL_LINUX || NACL_OSX
srandom(time(NULL));
#endif
VDiffInitializeAvailableDecoders();
nextarg = ParseArgv(argc, argv);
if (nextarg == argc) {
if (gPrefix == 0) RunRegressionTests();
TestAllInstructions();
} else {
int i;
gVerbose = TRUE;
for (i = nextarg; i < argc; ++i) {
TestOneInstruction(argv[i]);
}
}
PrintStats();
/* exit with non-zero error code if there were errors. */
exit(gVDiffStats.errors != 0);
}
static void
Test(const char *str)
{
char **av;
printf("Test: <%V>\n", str);
av = ParseArgv(str, 0);
PrintArgv(av);
}
int main(int argc, char *argv[])
{
char **input_files;
char *output_file;
char *arg_string;
int num_input_files;
int inmincid;
Loop_Options *loop_options;
Program_Data program_data;
/* Save time stamp and args */
arg_string = time_stamp(argc, argv);
/* Get arguments */
if (ParseArgv(&argc, argv, argTable, 0) || (argc < 3)) {
(void) fprintf(stderr,
"\nUsage: %s [options] <in1.mnc> [...] <out.mnc>\n",
argv[0]);
(void) fprintf(stderr,
" %s -help\n\n",
argv[0]);
exit(EXIT_FAILURE);
}
input_files = &argv[1];
num_input_files = argc - 2;
output_file = argv[argc-1];
/* Open the first input file and get the vector length */
inmincid = miopen(input_files[0], NC_NOWRITE);
if (get_vector_length(inmincid) > 1) {
(void) fprintf(stderr, "Input file %s is not a scalar file\n",
input_files[0]);
exit(EXIT_FAILURE);
}
/* Set up looping options */
loop_options = create_loop_options();
set_loop_clobber(loop_options, clobber);
set_loop_verbose(loop_options, verbose);
#if MINC2
set_loop_v2format(loop_options, v2format);
#endif /* MINC2 */
set_loop_datatype(loop_options, datatype, is_signed,
valid_range[0], valid_range[1]);
set_loop_output_vector_size(loop_options, num_input_files);
set_loop_buffer_size(loop_options, (long) buffer_size * 1024);
set_loop_first_input_mincid(loop_options, inmincid);
set_loop_accumulate(loop_options, TRUE, 0, NULL, NULL);
/* Do loop */
voxel_loop(num_input_files, input_files, 1, &output_file,
arg_string, loop_options,
do_makevector, (void *) &program_data);
exit(EXIT_SUCCESS);
}
void main(int argc, const char *argv[])
{
if (ParseArgv(argc, argv))
exit(1);
if (Options.printUsage)
PrintUsage(argv[0]);
else
StartModel();
exit(0);
}
int main(int argc, char *argv[])
{
VIO_General_transform gt;
char *xfmfile;
int i;
static ArgvInfo argTable[] = {
{"-center", ARGV_FLOAT, (char *) 3, (char *)cent,
"Force center of rotation and scale."},
{"-version", ARGV_FUNC, (char *) print_version_info, (char *)MNI_AUTOREG_LONG_VERSION,
"Print out version info and exit."},
{NULL, ARGV_END, NULL, NULL, NULL}
};
for(i=0; i<3; i++) {
cent[i] = 0.0;
}
if (ParseArgv(&argc, argv, argTable, 0) || (argc<2)) {
(void) fprintf(stderr, "Usage: %s file.xfm [file.mnc] [options] \n",
argv[0]);
exit(EXIT_FAILURE);
}
prog_name = argv[0];
xfmfile = argv[1];
if (argc>2) {
print ("mnc = %s\n",argv[2]);
if (! get_cog(argv[2], cent) ) {
print("Cannot calculate the COG of volume %s\n.", argv[2] );
exit(EXIT_FAILURE);
}
}
if (input_transform_file(xfmfile, >)!=VIO_OK) {
(void)fprintf(stderr, "Error reading transformation file.\n");
exit(EXIT_FAILURE);
}
process_general_transform( > );
exit(EXIT_SUCCESS);
}
TCGbool TCGClient::ParseArgFile(const TCGchar* fname, stCmdArgs &args)
{
auto_file f(fopen(fname, "r"));
TCGchar line[CMD_LEN] = {0};
TCGchar* argv[ARG_ITEMS]={NULL};
TCGbool loop = 1;
if (!f.file_)
{
TCGLOG(TCG_INFO, TCG_CLIENT_OS, "No config file TCGPlayer.conf @ /sdcard/Tencent/, use Default config replay");
return TCG_TRUE; //use default
}
fgets(line,CMD_LEN,f.file_);
if(line == NULL)
{
PrintHelp();
return TCG_FALSE;
}
//Handle use echo xxx > TCGPlayer.conf method generate config file
if (line[strlen(line)-1] == 10)
{
line[strlen(line)-1] = '\0';
}
argv[1] = strtok(line," ");
if(argv[1] == NULL)
{
argv[1] = line;
}
loop++;
while(loop < ARG_ITEMS)
{
argv[loop] = strtok(NULL," ");
if(argv[loop] == NULL) break;
loop++;
}
return ParseArgv(loop,argv,args);
}
int main(int argc, char *argv[])
{
Volume volume;
volume_input_struct input_info;
char *filename;
double v0, v1, v2, wx, wy, wz;
static char *dim_names[] =
{ANY_SPATIAL_DIMENSION, ANY_SPATIAL_DIMENSION, ANY_SPATIAL_DIMENSION};
milog_init(argv[0]);
/* Check arguments */
if (ParseArgv(&argc, argv, argTable, 0) || argc != 5) {
(void) fprintf(stderr,
"Usage: %s <image file> <voxel index 1 (slowest)> <index 2> <index 3>\n",
argv[0]);
exit(EXIT_FAILURE);
}
filename = argv[1];
v0 = atof(argv[2]);
v1 = atof(argv[3]);
v2 = atof(argv[4]);
/* Open the image file */
set_print_function(print_to_stderr);
if (start_volume_input(filename, 3, dim_names, MI_ORIGINAL_TYPE, TRUE,
0.0, 0.0, TRUE, &volume, NULL, &input_info) != OK) {
(void) fprintf(stderr, "Error opening file %s for input.\n",
filename);
exit(EXIT_FAILURE);
}
/* Convert the voxel to world coordinates */
convert_3D_voxel_to_world(volume, v0, v1, v2, &wx, &wy, &wz);
/* Write out the result */
(void) printf("%.20g %.20g %.20g\n", wx, wy, wz);
exit(EXIT_SUCCESS);
}
TCGbool TCGClient::Init(TCGint argc, TCGchar **argv, const TCGchar* fname)
{
#ifdef Android
if (!ParseArgFile(PLAY_CONF_FILE, g_args))
{
return ;
}
#elif defined(WIN32) || defined(__APPLE__)
if (!ParseArgv(argc, argv, g_args))
{
return TCG_FALSE;
}
#endif
GetScreenResolution();
GetScreenPosition();
ConnectServer();
m_stream.SetCompressFlag(g_args.compressedFile);
return TCG_TRUE;
}
int main(int argc, const char* argv[])
{
try
{
std::locale::global(std::locale("C"));
std::unique_ptr<Platform::Application> app(Platform::Application::Create());
return app->Run(ParseArgv(argc, argv));
}
catch (const Error& e)
{
StdOut << e.ToString() << std::endl;
return 1;
}
catch (const std::exception& e)
{
StdOut << e.what() << std::endl;
return 1;
}
catch (...)
{
StdOut << "Unhandled exception" << std::endl;
return 1;
}
}
int main(int argc, char *argv[])
{
char *infile, *outfile;
char *arg_string;
Loop_Options *loop_options;
int inmincid;
Lookup_Data lookup_data;
/* Save time stamp and args */
arg_string = time_stamp(argc, argv);
/* Get arguments */
if (ParseArgv(&argc, argv, argTable, 0) || (argc != 3)) {
(void) fprintf(stderr, "\nUsage: %s [options] <in.mnc> <out.mnc>\n",
argv[0]);
(void) fprintf(stderr, " %s -help\n\n",
argv[0]);
exit(EXIT_FAILURE);
}
infile = argv[1];
outfile = argv[2];
/* Get the appropriate lookup table */
if ((lookup_file != NULL) || (lookup_string != NULL)) {
lookup_data.lookup_table = read_lookup_table(lookup_file, lookup_string);
}
else {
switch (lookup_type) {
case LU_GRAY:
lookup_data.lookup_table = &gray_lookup;
break;
case LU_HOTMETAL:
lookup_data.lookup_table = &hotmetal_lookup;
break;
case LU_SPECTRAL:
lookup_data.lookup_table = &spectral_lookup;
break;
case LU_TABLE:
break;
default:
fprintf(stderr, "Unknown lookup type: %d\n", lookup_type);
break;
}
}
/* Get the null value */
lookup_data.null_value =
get_null_value(lookup_data.lookup_table->vector_length,
null_value_string);
/* Open the input file and get the range */
inmincid = miopen(infile, NC_NOWRITE);
if (!discrete_lookup && (lookup_range[0] == DEFAULT_RANGE)) {
get_full_range(inmincid, lookup_range);
}
if (lookup_min != DEFAULT_RANGE)
lookup_range[0] = lookup_min;
if (lookup_max != DEFAULT_RANGE)
lookup_range[1] = lookup_max;
/* Set up lookup information */
lookup_data.invert = invert_table;
lookup_data.range[0] = lookup_range[0];
lookup_data.range[1] = lookup_range[1];
lookup_data.discrete = discrete_lookup;
/* Set up looping options */
loop_options = create_loop_options();
set_loop_clobber(loop_options, clobber);
set_loop_verbose(loop_options, verbose);
#if MINC2
set_loop_v2format(loop_options, minc2_format);
#endif /* MINC2 */
set_loop_datatype(loop_options, datatype, is_signed,
valid_range[0], valid_range[1]);
set_loop_convert_input_to_scalar(loop_options, TRUE);
set_loop_output_vector_size(loop_options,
lookup_data.lookup_table->vector_length);
set_loop_buffer_size(loop_options, (long) buffer_size * 1024);
set_loop_first_input_mincid(loop_options, inmincid);
/* Do loop */
voxel_loop(1, &infile, 1, &outfile, arg_string, loop_options,
do_lookup, (void *) &lookup_data);
/* Free stuff */
if (lookup_data.null_value != NULL) free(lookup_data.null_value);
if (lookup_data.lookup_table->free_data) {
free(lookup_data.lookup_table->table);
free(lookup_data.lookup_table);
}
exit(EXIT_SUCCESS);
}
int
main(int argc, char **argv)
{
/* NIFTI stuff */
nifti_image *nii_ptr;
nifti_image nii_rec;
int nii_dimids[MAX_NII_DIMS];
int nii_dir[MAX_NII_DIMS];
int nii_map[MAX_NII_DIMS];
unsigned long nii_lens[MAX_NII_DIMS];
int nii_ndims;
static int nifti_filetype;
static int nifti_datatype;
static int nifti_signed = 1;
/* MINC stuff */
int mnc_fd; /* MINC file descriptor */
nc_type mnc_type; /* MINC data type as read */
int mnc_ndims; /* MINC image dimension count */
int mnc_dimids[MAX_VAR_DIMS]; /* MINC image dimension identifiers */
long mnc_dlen; /* MINC dimension length value */
double mnc_dstep; /* MINC dimension step value */
int mnc_icv; /* MINC image conversion variable */
int mnc_vid; /* MINC Image variable ID */
long mnc_start[MAX_VAR_DIMS]; /* MINC data starts */
long mnc_count[MAX_VAR_DIMS]; /* MINC data counts */
int mnc_signed; /* MINC if output voxels are signed */
double real_range[2]; /* MINC real range (min, max) */
double input_valid_range[2]; /* MINC valid range (min, max) */
double output_valid_range[2]; /* Valid range of output data. */
double nifti_slope; /* Slope to be applied to output voxels. */
double nifti_inter; /* Intercept to be applied to output voxels. */
double total_valid_range; /* Overall valid range (max - min). */
double total_real_range; /* Overall real range (max - min). */
/* Other stuff */
char out_str[1024]; /* Big string for filename */
char att_str[1024]; /* Big string for attribute values */
int i; /* Generic loop counter the first */
int j; /* Generic loop counter the second */
char *str_ptr; /* Generic ASCIZ string pointer */
int r; /* Result code. */
static int vflag = 0; /* Verbose flag (default is quiet) */
static ArgvInfo argTable[] = {
{NULL, ARGV_HELP, NULL, NULL,
"Output voxel data type specification"},
{"-byte", ARGV_CONSTANT, (char *)DT_INT8, (char *)&nifti_datatype,
"Write voxel data in 8-bit signed integer format."},
{"-short", ARGV_CONSTANT, (char *)DT_INT16, (char *)&nifti_datatype,
"Write voxel data in 16-bit signed integer format."},
{"-int", ARGV_CONSTANT, (char *)DT_INT32, (char *)&nifti_datatype,
"Write voxel data in 32-bit signed integer format."},
{"-float", ARGV_CONSTANT, (char *)DT_FLOAT32, (char *)&nifti_datatype,
"Write voxel data in 32-bit floating point format."},
{"-double", ARGV_CONSTANT, (char *)DT_FLOAT64, (char *)&nifti_datatype,
"Write voxel data in 64-bit floating point format."},
{"-signed", ARGV_CONSTANT, (char *)1, (char *)&nifti_signed,
"Write integer voxel data in signed format."},
{"-unsigned", ARGV_CONSTANT, (char *)0, (char *)&nifti_signed,
"Write integer voxel data in unsigned format."},
{NULL, ARGV_HELP, NULL, NULL,
"Output file format specification"},
{"-dual", ARGV_CONSTANT, (char *)FT_NIFTI_DUAL,
(char *)&nifti_filetype,
"Write NIfTI-1 two-file format (.img and .hdr)"},
{"-ASCII", ARGV_CONSTANT, (char *)FT_NIFTI_ASCII,
(char *)&nifti_filetype,
"Write NIfTI-1 ASCII header format (.nia)"},
{"-nii", ARGV_CONSTANT, (char *)FT_NIFTI_SINGLE,
(char *)&nifti_filetype,
"Write NIfTI-1 one-file format (.nii)"},
{"-analyze", ARGV_CONSTANT, (char *)FT_ANALYZE,
(char *)&nifti_filetype,
"Write an Analyze two-file format file (.img and .hdr)"},
{NULL, ARGV_HELP, NULL, NULL,
"Other options"},
{"-quiet", ARGV_CONSTANT, (char *)0,
(char *)&vflag,
"Quiet operation"},
{"-verbose", ARGV_CONSTANT, (char *)1,
(char *)&vflag,
"Quiet operation"},
{NULL, ARGV_END, NULL, NULL, NULL}
};
ncopts = 0; /* Clear global netCDF error reporting flag */
/* Default NIfTI file type is "NII", single binary file
*/
nifti_filetype = FT_UNSPECIFIED;
nifti_datatype = DT_UNKNOWN;
if (ParseArgv(&argc, argv, argTable, 0) || (argc < 2)) {
fprintf(stderr, "Too few arguments\n");
return usage();
}
if (!nifti_signed) {
switch (nifti_datatype) {
case DT_INT8:
nifti_datatype = DT_UINT8;
break;
case DT_INT16:
nifti_datatype = DT_UINT16;
break;
case DT_INT32:
nifti_datatype = DT_UINT32;
break;
}
}
switch (nifti_datatype){
case DT_INT8:
case DT_UINT8:
mnc_type = NC_BYTE;
break;
case DT_INT16:
case DT_UINT16:
mnc_type = NC_SHORT;
break;
case DT_INT32:
case DT_UINT32:
mnc_type = NC_INT;
break;
case DT_FLOAT32:
mnc_type = NC_FLOAT;
break;
case DT_FLOAT64:
mnc_type = NC_DOUBLE;
break;
}
if (argc == 2) {
strcpy(out_str, argv[1]);
str_ptr = strrchr(out_str, '.');
if (str_ptr != NULL && !strcmp(str_ptr, ".mnc")) {
*str_ptr = '\0';
}
}
else if (argc == 3) {
strcpy(out_str, argv[2]);
str_ptr = strrchr(out_str, '.');
if (str_ptr != NULL) {
/* See if a recognized file extension was specified. If so,
* we trim it off and set the output file type if none was
* specified. If the extension is not recognized, assume
* that we will form the filename by just adding the right
* extension for the selected output format.
*/
if (!strcmp(str_ptr, ".nii")) {
if (nifti_filetype == FT_UNSPECIFIED) {
nifti_filetype = FT_NIFTI_SINGLE;
}
*str_ptr = '\0';
}
else if (!strcmp(str_ptr, ".img") ||
!strcmp(str_ptr, ".hdr")) {
if (nifti_filetype == FT_UNSPECIFIED) {
nifti_filetype = FT_NIFTI_DUAL;
}
*str_ptr = '\0';
}
else if (!strcmp(str_ptr, ".nia")) {
if (nifti_filetype == FT_UNSPECIFIED) {
nifti_filetype = FT_NIFTI_ASCII;
}
*str_ptr = '\0';
}
}
}
else {
fprintf(stderr, "Filename argument required\n");
return usage();
}
/* Open the MINC file. It needs to exist.
*/
mnc_fd = miopen(argv[1], NC_NOWRITE);
if (mnc_fd < 0) {
fprintf(stderr, "Can't find input file '%s'\n", argv[1]);
return (-1);
}
/* Find the MINC image variable. If we can't find it, there is no
* further processing possible...
*/
mnc_vid = ncvarid(mnc_fd, MIimage);
if (mnc_vid < 0) {
fprintf(stderr, "Can't locate the image variable (mnc_vid=%d)\n", mnc_vid);
return (-1);
}
/* Find out about the MINC image variable - specifically, how many
* dimensions, and which dimensions.
*/
r = ncvarinq(mnc_fd, mnc_vid, NULL, NULL, &mnc_ndims, mnc_dimids, NULL);
if (r < 0) {
fprintf(stderr, "Can't read information from image variable\n");
return (-1);
}
if (mnc_ndims > MAX_NII_DIMS) {
fprintf(stderr, "NIfTI-1 files may contain at most %d dimensions\n",
MAX_NII_DIMS);
return (-1);
}
/* Initialize the NIfTI structure
*/
nii_ptr = &nii_rec;
init_nifti_header(nii_ptr);
/* For now we just use the mnc2nii command line as the description
* field. Probably we should use something better, perhaps a
* combination of some other standard MINC fields that might
* provide more information.
*/
str_ptr = nii_ptr->descrip;
for (i = 0; i < argc; i++) {
char *arg_ptr = argv[i];
if ((str_ptr - nii_ptr->descrip) >= MAX_NII_DESCRIP) {
break;
}
if (i != 0) {
*str_ptr++ = ' ';
}
while (*arg_ptr != '\0' &&
(str_ptr - nii_ptr->descrip) < MAX_NII_DESCRIP) {
*str_ptr++ = *arg_ptr++;
}
*str_ptr = '\0';
}
nii_ptr->fname = malloc(strlen(out_str) + 4 + 1);
nii_ptr->iname = malloc(strlen(out_str) + 4 + 1);
strcpy(nii_ptr->fname, out_str);
strcpy(nii_ptr->iname, out_str);
switch (nifti_filetype) {
case FT_ANALYZE:
strcat(nii_ptr->fname, ".hdr");
strcat(nii_ptr->iname, ".img");
break;
case FT_NIFTI_SINGLE:
strcat(nii_ptr->fname, ".nii");
strcat(nii_ptr->iname, ".nii");
break;
case FT_NIFTI_DUAL:
strcat(nii_ptr->fname, ".hdr");
strcat(nii_ptr->iname, ".img");
break;
case FT_NIFTI_ASCII:
strcat(nii_ptr->fname, ".nia");
strcat(nii_ptr->iname, ".nia");
break;
default:
fprintf(stderr, "Unknown output file type %d\n", nifti_filetype);
return (-1);
}
/* Get real voxel range for the input file.
*/
miget_image_range(mnc_fd, real_range);
/* Get the actual valid voxel value range.
*/
miget_valid_range(mnc_fd, mnc_vid, input_valid_range);
/* Find the default range for the output type. Our output file
* will use the full legal range of the output type if it is
* an integer.
*/
if (nifti_datatype == DT_UNKNOWN) {
nii_ptr->datatype = DT_FLOAT32; /* Default */
mnc_type = NC_FLOAT;
mnc_signed = 1;
}
else {
nii_ptr->datatype = nifti_datatype;
mnc_signed = nifti_signed;
}
if (vflag) {
fprintf(stderr, "MINC type %d signed %d\n", mnc_type, mnc_signed);
}
miget_default_range(mnc_type, mnc_signed, output_valid_range);
total_valid_range = input_valid_range[1] - input_valid_range[0];
total_real_range = real_range[1] - real_range[0];
if ((output_valid_range[1] - output_valid_range[0]) > total_valid_range) {
/* Empirically, forcing the valid range to be the nearest power
* of two greater than the existing valid range seems to improve
* the behavior of the conversion. This is at least in part because
* of the limited precision of the NIfTI-1 voxel scaling fields.
*/
double new_range = nearest_power_of_two(total_valid_range);
if (new_range - 1.0 >= total_valid_range) {
new_range -= 1.0;
}
if (output_valid_range[1] > total_valid_range) {
output_valid_range[0] = 0;
output_valid_range[1] = new_range;
}
else {
output_valid_range[1] = output_valid_range[0] + new_range;
}
}
else {
/* The new range can't fully represent the input range. Use the
* full available range, and warn the user that they may have a
* problem.
*/
printf("WARNING: Range of input exceeds range of output format.\n");
}
if (vflag) {
printf("Real range: %f %f Input valid range: %f %f Output valid range: %f %f\n",
real_range[0], real_range[1],
input_valid_range[0], input_valid_range[1],
output_valid_range[0], output_valid_range[1]);
}
/* If the output type is not floating point, we may need to scale the
* voxel values.
*/
if (mnc_type != NC_FLOAT && mnc_type != NC_DOUBLE) {
/* Figure out how to map pixel values into the range of the
* output datatype.
*/
nifti_slope = ((real_range[1] - real_range[0]) /
(output_valid_range[1] - output_valid_range[0]));
if (nifti_slope == 0.0) {
nifti_slope = 1.0;
}
nifti_inter = real_range[0] - (output_valid_range[0] * nifti_slope);
/* One problem with NIfTI-1 is the limited precision of the
* scl_slope and scl_inter fields (they are just 32-bits). So
* we look for possible issues and warn about that here.
*/
if (nifti_inter != (float) nifti_inter ||
nifti_slope != (float) nifti_slope) {
double epsilon_i = nifti_inter - (float) nifti_inter;
double epsilon_s = nifti_slope - (float) nifti_slope;
/* If the loss in precision is more than one part per thousand
* of the real range, flag this as a problem!
*/
if ((epsilon_i > total_real_range / 1.0e3) ||
(epsilon_s > total_real_range / 1.0e3)) {
fprintf(stderr, "ERROR: Slope and intercept cannot be represented in the NIfTI-1 header.\n");
fprintf(stderr, " slope %f (%f), intercept %f (%f)\n",
nifti_slope, (float) nifti_slope,
nifti_inter, (float) nifti_inter);
return (-1);
}
}
}
else {
nifti_slope = 0.0;
}
nii_ptr->scl_slope = nifti_slope;
nii_ptr->scl_inter = nifti_inter;
nii_ptr->nvox = 1; /* Initial value for voxel count */
/* Find all of the dimensions of the MINC file, in the order they
* will be listed in the NIfTI-1/Analyze file. We use this to build
* a map for restructuring the data according to the normal rules
* of NIfTI-1.
*/
nii_ndims = 0;
for (i = 0; i < MAX_NII_DIMS; i++) {
if (dimnames[i] == NULL) {
nii_dimids[nii_ndims] = -1;
continue;
}
nii_dimids[nii_ndims] = ncdimid(mnc_fd, dimnames[i]);
if (nii_dimids[nii_ndims] == -1) {
continue;
}
/* Make sure the dimension is actually used to define the image.
*/
for (j = 0; j < mnc_ndims; j++) {
if (nii_dimids[nii_ndims] == mnc_dimids[j]) {
nii_map[nii_ndims] = j;
break;
}
}
if (j < mnc_ndims) {
mnc_dlen = 1;
mnc_dstep = 0;
ncdiminq(mnc_fd, nii_dimids[nii_ndims], NULL, &mnc_dlen);
ncattget(mnc_fd, ncvarid(mnc_fd, dimnames[i]), MIstep, &mnc_dstep);
if (mnc_dstep < 0) {
nii_dir[nii_ndims] = -1;
mnc_dstep = -mnc_dstep;
}
else {
nii_dir[nii_ndims] = 1;
}
nii_lens[nii_ndims] = mnc_dlen;
nii_ndims++;
}
nii_ptr->dim[dimmap[i]] = (int) mnc_dlen;
nii_ptr->nvox *= mnc_dlen;
nii_ptr->pixdim[dimmap[i]] = (float) mnc_dstep;
}
/* Here we do some "post-processing" of the results. Make certain that
* the nt value is never zero, and make certain that ndim is set to
* 4 if there is a time dimension and 5 if there is a vector dimension
*/
if (nii_ptr->dim[3] > 1 && nii_ndims < 4) {
nii_ndims = 4;
}
if (nii_ptr->dim[4] > 1) {
nii_ptr->intent_code = NIFTI_INTENT_VECTOR;
nii_ndims = 5;
}
nii_ptr->ndim = nii_ndims; /* Total number of dimensions in file */
nii_ptr->nx = nii_ptr->dim[0];
nii_ptr->ny = nii_ptr->dim[1];
nii_ptr->nz = nii_ptr->dim[2];
nii_ptr->nt = nii_ptr->dim[3];
nii_ptr->nu = nii_ptr->dim[4];
nii_ptr->dx = nii_ptr->pixdim[0];
nii_ptr->dy = nii_ptr->pixdim[1];
nii_ptr->dz = nii_ptr->pixdim[2];
nii_ptr->dt = nii_ptr->pixdim[3];
nii_ptr->du = 1; /* MINC files don't define a sample size for a vector_dimension */
nii_ptr->nifti_type = nifti_filetype;
/* Load the direction_cosines and start values into the NIfTI-1
* sform structure.
*
*/
for (i = 0; i < MAX_SPACE_DIMS; i++) {
int id = ncvarid(mnc_fd, mnc_spatial_names[i]);
double start;
double step;
double dircos[MAX_SPACE_DIMS];
int tmp;
if (id < 0) {
continue;
}
/* Set default values */
start = 0.0;
step = 1.0;
dircos[DIM_X] = dircos[DIM_Y] = dircos[DIM_Z] = 0.0;
dircos[i] = 1.0;
miattget(mnc_fd, id, MIstart, NC_DOUBLE, 1, &start, &tmp);
miattget(mnc_fd, id, MIstep, NC_DOUBLE, 1, &step, &tmp);
miattget(mnc_fd, id, MIdirection_cosines, NC_DOUBLE, MAX_SPACE_DIMS,
dircos, &tmp);
ncdiminq(mnc_fd, ncdimid(mnc_fd, mnc_spatial_names[i]), NULL,
&mnc_dlen);
if (step < 0) {
step = -step;
start = start - step * (mnc_dlen - 1);
}
nii_ptr->sto_xyz.m[0][i] = step * dircos[0];
nii_ptr->sto_xyz.m[1][i] = step * dircos[1];
nii_ptr->sto_xyz.m[2][i] = step * dircos[2];
nii_ptr->sto_xyz.m[0][3] += start * dircos[0];
nii_ptr->sto_xyz.m[1][3] += start * dircos[1];
nii_ptr->sto_xyz.m[2][3] += start * dircos[2];
miattgetstr(mnc_fd, id, MIspacetype, sizeof(att_str), att_str);
/* Try to set the S-transform code correctly.
*/
if (!strcmp(att_str, MI_TALAIRACH)) {
nii_ptr->sform_code = NIFTI_XFORM_TALAIRACH;
}
else if (!strcmp(att_str, MI_CALLOSAL)) {
/* TODO: Not clear what do do here... */
nii_ptr->sform_code = NIFTI_XFORM_SCANNER_ANAT;
}
else { /* MI_NATIVE or unknown */
nii_ptr->sform_code = NIFTI_XFORM_SCANNER_ANAT;
}
}
/* So the last row is right... */
nii_ptr->sto_xyz.m[3][0] = 0.0;
nii_ptr->sto_xyz.m[3][1] = 0.0;
nii_ptr->sto_xyz.m[3][2] = 0.0;
nii_ptr->sto_xyz.m[3][3] = 1.0;
nii_ptr->sto_ijk = nifti_mat44_inverse(nii_ptr->sto_xyz);
nifti_datatype_sizes(nii_ptr->datatype,
&nii_ptr->nbyper, &nii_ptr->swapsize);
if (vflag) {
nifti_image_infodump(nii_ptr);
}
/* Now load the actual MINC data. */
nii_ptr->data = malloc(nii_ptr->nbyper * nii_ptr->nvox);
if (nii_ptr->data == NULL) {
fprintf(stderr, "Out of memory.\n");
return (-1);
}
mnc_icv = miicv_create();
miicv_setint(mnc_icv, MI_ICV_TYPE, mnc_type);
miicv_setstr(mnc_icv, MI_ICV_SIGN, (mnc_signed) ? MI_SIGNED : MI_UNSIGNED);
miicv_setdbl(mnc_icv, MI_ICV_VALID_MAX, output_valid_range[1]);
miicv_setdbl(mnc_icv, MI_ICV_VALID_MIN, output_valid_range[0]);
miicv_setdbl(mnc_icv, MI_ICV_IMAGE_MAX, real_range[1]);
miicv_setdbl(mnc_icv, MI_ICV_IMAGE_MIN, real_range[0]);
miicv_setdbl(mnc_icv, MI_ICV_DO_NORM, TRUE);
miicv_setdbl(mnc_icv, MI_ICV_USER_NORM, TRUE);
miicv_attach(mnc_icv, mnc_fd, mnc_vid);
/* Read in the entire hyperslab from the file.
*/
for (i = 0; i < mnc_ndims; i++) {
ncdiminq(mnc_fd, mnc_dimids[i], NULL, &mnc_count[i]);
mnc_start[i] = 0;
}
r = miicv_get(mnc_icv, mnc_start, mnc_count, nii_ptr->data);
if (r < 0) {
fprintf(stderr, "Read error\n");
return (-1);
}
/* Shut down the MINC stuff now that it has done its work.
*/
miicv_detach(mnc_icv);
miicv_free(mnc_icv);
miclose(mnc_fd);
if (vflag) {
/* Debugging stuff - just to check the contents of these arrays.
*/
for (i = 0; i < nii_ndims; i++) {
printf("%d: %ld %d %d\n",
i, nii_lens[i], nii_map[i], nii_dir[i]);
}
printf("bytes per voxel %d\n", nii_ptr->nbyper);
printf("# of voxels %ld\n", nii_ptr->nvox);
}
/* Rearrange the data to correspond to the NIfTI dimension ordering.
*/
restructure_array(nii_ndims,
nii_ptr->data,
nii_lens,
nii_ptr->nbyper,
nii_map,
nii_dir);
if (vflag) {
/* More debugging stuff - check coordinate transform.
*/
test_xform(nii_ptr->sto_xyz, 0, 0, 0);
test_xform(nii_ptr->sto_xyz, 10, 0, 0);
test_xform(nii_ptr->sto_xyz, 0, 10, 0);
test_xform(nii_ptr->sto_xyz, 0, 0, 10);
test_xform(nii_ptr->sto_xyz, 10, 10, 10);
}
if (vflag) {
fprintf(stdout, "Writing NIfTI-1 file...");
}
nifti_image_write(nii_ptr);
if (vflag) {
fprintf(stdout, "done.\n");
}
return (0);
}
int
main(int argc, char *argv[])
{
int r;
const char **file_list = NULL; /* List of file names */
struct vff_attrs vffattrs;
struct mnc_vars mnc2;
char out_str[1024]; /* Big string for filename */
midimhandle_t hdim[MAX_VFF_DIMS];
mihandle_t hvol;
double mnc_vrange[2]; /* MINC valid min/max */
int num_file_args; /* Number of files on command line */
string_t out_dir; /* Output directory */
int length;
struct stat st;
int ifile;
int num_files; /* Total number of files */
int is_file=0;
int is_list=0;
int ival;
char *extension;
mnc2.mnc_srange[0]= -1;
mnc2.mnc_srange[1]= -1;
G.pname = argv[0]; /* get program name */
G.dirname = NULL;
G.little_endian = 1; /*default is little endian unless otherwise*/
G.minc_history = time_stamp(argc, argv); /* Create minc history string */
if (ParseArgv(&argc, argv, argTable, 0) || argc < 2) {
usage();
exit(EXIT_FAILURE);
}
if (G.dirname != NULL) {
#if HAVE_DIRENT_H
if (stat(G.dirname, &st) != 0 || !S_ISDIR(st.st_mode)) {
fprintf(stderr,"Option -addattrs requires directory as argument!!!\n");
exit(EXIT_FAILURE);
}
#endif
}
if (G.List)
{
num_file_args = argc - 1;
}
else
{
strcpy(out_str, argv[1]);
extension = strrchr(out_str, '.');
if (extension != NULL )
{
extension++;
if (strcmp(extension, "mnc") !=0)
{
usage();
exit(EXIT_FAILURE);
}
}
if (argc == 3)
{
/* check if last argument is dir */
num_file_args = argc - 2;
strcpy(out_dir, argv[argc - 1]);
/* make sure path ends with slash
*/
length = strlen(out_dir);
if (out_dir[length - 1] != '/')
{
out_dir[length++] = '/';
out_dir[length++] = '\0';
}
if (stat(out_dir, &st) != 0 || !S_ISDIR(st.st_mode))
{/* assume filename */
is_file =1;
}
}
else
{ //list of 2d files must check!
num_file_args = argc - 2;
is_list = 1;
}
}
if (!is_file || G.List)
{
/* Get space for file lists */
/* Allocate the array of pointers used to implement the
* list of filenames.
*/
file_list = malloc(1 * sizeof(char *));
CHKMEM(file_list);
/* Go through the list of files, expanding directories where they
* are encountered...
*/
num_files = 0;
for (ifile = 1 ; ifile <= num_file_args; ifile++)
{
#if HAVE_DIRENT_H
if (stat(argv[ifile + 1], &st) == 0 && S_ISDIR(st.st_mode))
{
DIR *dp;
struct dirent *np;
char *tmp_str;
length = strlen(argv[ifile + 1]);
dp = opendir(argv[ifile + 1]);
if (dp != NULL)
{
while ((np = readdir(dp)) != NULL)
{
/* Generate the full path to the file.
*/
tmp_str = malloc(length + strlen(np->d_name) + 2);
strcpy(tmp_str, argv[ifile + 1]);
if (tmp_str[length-1] != '/')
{
tmp_str[length] = '/';
tmp_str[length+1] = '\0';
}
strcat(&tmp_str[length], np->d_name);
if (stat(tmp_str, &st) == 0 && S_ISREG(st.st_mode))
{
file_list = realloc(file_list,
(num_files + 1) * sizeof(char *));
file_list[num_files++] = tmp_str;
}
else
{
free(tmp_str);
}
}
closedir(dp);
}
else
{
fprintf(stderr, "Error opening directory '%s'\n",
argv[ifile + 1]);
}
}
else
{
file_list = realloc(file_list, (num_files + 1) * sizeof(char *));
file_list[num_files++] = strdup(argv[ifile + 1]);
}
#else
file_list = realloc(file_list, (num_files + 1) * sizeof(char *));
file_list[num_files++] = strdup(argv[ifile + 1]);
#endif
}
}
if (G.List)
{
exit(EXIT_SUCCESS);
}
if (is_file)
{
read_3Dvff_file_header(argv[2],&mnc2,&vffattrs);
}
else
{
read_2Dvff_files_header(file_list,num_files,&mnc2,&vffattrs);
}
/* ok starting to create minc2.0 file assuming 3D must take care of 2D*/
r = micreate_dimension("zspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, mnc2.mnc_count[2], &hdim[0]);
if (r != 0) {
TESTRPT("failed create_dimension zspace", r);
return (1);
}
r = micreate_dimension("yspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, mnc2.mnc_count[1], &hdim[1]);
if (r != 0) {
TESTRPT("failed create_dimension yspace", r);
return (1);
}
r = micreate_dimension("xspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, mnc2.mnc_count[0], &hdim[2]);
if (r != 0) {
TESTRPT("failed create_dimension xspace", r);
return (1);
}
r = miset_dimension_start(hdim[0], mnc2.mnc_starts[2]);
if (r < 0) {
TESTRPT("failed dimension start xspace", r);
return (1);
}
r = miset_dimension_start(hdim[1], mnc2.mnc_starts[1]);
if (r < 0) {
TESTRPT("failed dimension start yspace", r);
return (1);
}
/* create negative start for xspace to correct orientation */
r = miset_dimension_start(hdim[2], mnc2.mnc_starts[0] * -1);
if (r < 0) {
TESTRPT("failed dimension start zspace", r);
return (1);
}
/* create negative spacing for zspace to correct orientation */
r = miset_dimension_separation(hdim[0], mnc2.mnc_steps[2] * -1);
if (r < 0) {
TESTRPT("failed dimension separation xspace", r);
return (1);
}
/* create negative spacing for yspace to correct orientation */
r = miset_dimension_separation(hdim[1], mnc2.mnc_steps[1] * -1);
if (r < 0) {
TESTRPT("failed dimension separation yspace", r);
return (1);
}
r = miset_dimension_separation(hdim[2], mnc2.mnc_steps[0]);
if (r < 0) {
TESTRPT("failed dimension separation zspace", r);
return (1);
}
r = micreate_volume(out_str,MAX_VFF_DIMS, hdim, mnc2.mnc_type,
MI_CLASS_REAL, NULL, &hvol);
if (r != 0) {
TESTRPT("error creating volume", r);
return (1);
}
r = micreate_volume_image(hvol);
if (r != 0) {
TESTRPT("error creating volume", r);
return (1);
}
// read image slice by slice
if (is_file)
{
read_3Dvff_file_image(hvol, argv[2], mnc2, vffattrs, mnc_vrange);
}
else
{
read_2Dvff_files_image(hvol,file_list,num_files, mnc2, vffattrs, mnc_vrange);
}
miset_volume_valid_range(hvol,mnc_vrange[1], mnc_vrange[0]);
if (mnc2.mnc_srange[0] == -1 || mnc2.mnc_srange[1] == -1) {
/* min and max are not specified in the file
voxel range is set same as real range */
mnc2.mnc_srange[0] = mnc_vrange[0];
mnc2.mnc_srange[1] = mnc_vrange[1];
}
miset_volume_range(hvol,mnc2.mnc_srange[1], mnc2.mnc_srange[0]);
if (is_file) {
/* create minc history 3D */
strcat(vffattrs.cmd_line,G.minc_history);
G.minc_history = vffattrs.cmd_line;
/* attributes from vff file itself 3D case*/
add_vff_attribute_to_file(hvol,&vffattrs);
}
if (G.dirname != NULL) {
/* attributes from external files 3D case*/
add_attributes_from_files(hvol);
}
else if (!is_file) {
/* just afew attributes from 2D case */
ival = vffattrs.year;
r = miset_attr_values(hvol, MI_TYPE_INT, "study",
MIstart_year,1 , &ival);
if (r < 0) {
TESTRPT("failed to add date:year attribute", r);
}
ival = vffattrs.month;
r = miset_attr_values(hvol, MI_TYPE_INT, "study",
MIstart_month,1 , &ival);
if (r < 0) {
TESTRPT("failed to add date:month attribute", r);
}
ival = vffattrs.day;
r = miset_attr_values(hvol, MI_TYPE_INT, "study",
MIstart_day,1 , &ival);
if (r < 0) {
TESTRPT("failed to add date:day attribute", r);
}
}
/* add history attribute */
r = miadd_history_attr(hvol,strlen(G.minc_history), G.minc_history);
if (r < 0) {
TESTRPT("error creating history", r);
return (1);
}
if (file_list != NULL) {
free_list(num_files, file_list);
free(file_list);
}
miclose_volume(hvol);
exit(EXIT_SUCCESS);
}
int main(int argc, char *argv[])
{
char **infiles;
int n_infiles;
char *out_fn;
char *history;
VIO_progress_struct progress;
VIO_Volume totals, weights;
int i, j, k, v;
double min, max;
double w_min, w_max;
long num_missed;
double weight, value;
double initial_weight;
VIO_Real dummy[3];
int sizes[MAX_VAR_DIMS];
double starts[MAX_VAR_DIMS];
double steps[MAX_VAR_DIMS];
long t = 0;
/* start the time counter */
current_realtime_seconds();
/* get the history string */
history = time_stamp(argc, argv);
/* get args */
if(ParseArgv(&argc, argv, argTable, 0) || (argc < 3)){
fprintf(stderr,
"\nUsage: %s [options] <in1.mnc> [<in2.mnc> [...]] <out.mnc>\n", argv[0]);
fprintf(stderr,
" %s [options] -arb_path pth.conf <infile.raw> <out.mnc>\n", argv[0]);
fprintf(stderr, " %s -help\n\n", argv[0]);
exit(EXIT_FAILURE);
}
/* get file names */
n_infiles = argc - 2;
infiles = (char **)malloc(sizeof(char *) * n_infiles);
for(i = 0; i < n_infiles; i++){
infiles[i] = argv[i + 1];
}
out_fn = argv[argc - 1];
/* check for infiles and outfile */
for(i = 0; i < n_infiles; i++){
if(!file_exists(infiles[i])){
fprintf(stderr, "%s: Couldn't find input file %s.\n\n", argv[0], infiles[i]);
exit(EXIT_FAILURE);
}
}
if(!clobber && file_exists(out_fn)){
fprintf(stderr, "%s: %s exists, -clobber to overwrite.\n\n", argv[0], out_fn);
exit(EXIT_FAILURE);
}
/* check for weights_fn if required */
if(weights_fn != NULL){
if(!clobber && file_exists(weights_fn)){
fprintf(stderr, "%s: %s exists, -clobber to overwrite.\n\n", argv[0],
weights_fn);
exit(EXIT_FAILURE);
}
}
/* set up parameters for reconstruction */
if(out_dtype == NC_UNSPECIFIED){
out_dtype = in_dtype;
}
if(out_is_signed == DEF_BOOL){
out_is_signed = in_is_signed;
}
/* check vector dimension size */
if(vect_size < 1){
fprintf(stderr, "%s: -vector (%d) must be 1 or greater.\n\n", argv[0], vect_size);
exit(EXIT_FAILURE);
}
/* check sigma */
if(regrid_sigma[0] <= 0 || regrid_sigma[1] <= 0 || regrid_sigma[2] <= 0 ){
fprintf(stderr, "%s: -sigma must be greater than 0\n\n", argv[0]);
exit(EXIT_FAILURE);
}
/* read in the output file config from a file is specified */
if(out_config_fn != NULL){
int ext_args_c;
char *ext_args[32]; /* max possible is 32 arguments */
ext_args_c = read_config_file(out_config_fn, ext_args);
if(ParseArgv(&ext_args_c, ext_args, argTable,
ARGV_DONT_SKIP_FIRST_ARG | ARGV_NO_LEFTOVERS | ARGV_NO_DEFAULTS)){
fprintf(stderr, "\nError in parameters in %s\n", out_config_fn);
exit(EXIT_FAILURE);
}
}
if(verbose){
fprintf_vol_def(stdout, &out_inf);
}
/* transpose the geometry arrays */
/* out_inf.*[] are in world xyz order, perm[] is the permutation
array to map world xyz to the right voxel order in the volume */
for(i = 0; i < WORLD_NDIMS; i++){
sizes[i] = out_inf.nelem[perm[i]]; /* sizes, starts, steps are in voxel volume order. */
starts[i] = out_inf.start[perm[i]];
steps[i] = out_inf.step[perm[i]];
}
sizes[WORLD_NDIMS] = vect_size;
/* create the totals volume */
totals = create_volume((vect_size > 1) ? 4 : 3,
(vect_size > 1) ? std_dimorder_v : std_dimorder,
out_dtype, out_is_signed, 0.0, 0.0);
set_volume_sizes(totals, sizes);
set_volume_starts(totals, starts);
set_volume_separations(totals, steps);
for(i = 0; i < WORLD_NDIMS; i++){
/* out_inf.dircos is in world x,y,z order, we have to use the perm array to
map each direction to the right voxel axis. */
set_volume_direction_cosine(totals, i, out_inf.dircos[perm[i]]);
}
alloc_volume_data(totals);
/* create the "weights" volume */
weights = create_volume(3, std_dimorder, out_dtype, out_is_signed, 0.0, 0.0);
set_volume_sizes(weights, sizes);
set_volume_starts(weights, starts);
set_volume_separations(weights, steps);
for(i = 0; i < WORLD_NDIMS; i++){
set_volume_direction_cosine(weights, i, out_inf.dircos[perm[i]]);
}
alloc_volume_data(weights);
/* down below in regrid_loop, Andrew makes a nasty direct reference to the
voxel_to_world transformation in the volume. This
transformation is not necessarily up to date, particularly when
non-default direction cosines are used. In volume_io, the
direction cosines are set and a FLAG is also set to indicate
that the voxel-to-world xform is not up to date. If the stanrd
volume_io general transform code is used, it checks internally
to see if the matrix is up to date, and if not it is recomputed.
So here, we'll (LC + MK) force an update by calling a general
transform. */
// convert_world_to_voxel(weights, (Real) 0, (Real) 0, (Real) 0, dummy);
// convert_world_to_voxel(totals, (Real) 0, (Real) 0, (Real) 0, dummy);
fprintf(stderr, "2Sizes: [%d:%d:%d] \n", sizes[perm[0]], sizes[perm[1]], sizes[perm[2]]);
/* initialize weights to be arbitray large value if using NEAREST */
/* volume interpolation else initialize all to zero */
if(regrid_type == NEAREST_FUNC && ap_coord_fn == NULL){
initial_weight = LARGE_INITIAL_WEIGHT;
}
else{
initial_weight = 0.0;
}
/* initialize weights and totals */
for(k = sizes[Z_IDX]; k--;){
for(j = sizes[Y_IDX]; j--;){
for(i = sizes[X_IDX]; i--;){
set_volume_real_value(weights, k, j, i, 0, 0, initial_weight);
for(v = vect_size; v--;){
set_volume_real_value(totals, k, j, i, v, 0, 0.0);
}
}
}
}
/* if regridding via an arbitrary path */
if(ap_coord_fn != NULL){
if(n_infiles > 1){
fprintf(stderr, "%s: arb_path only works for one input file (so far).\n\n",
argv[0]);
exit(EXIT_FAILURE);
}
/* print some pretty output */
if(verbose){
fprintf(stdout, " | Input data: %s\n", infiles[0]);
fprintf(stdout, " | Arb path: %s\n", ap_coord_fn);
fprintf(stdout, " | Output range: [%g:%g]\n", out_range[0], out_range[1]);
fprintf(stdout, " | Output file: %s\n", out_fn);
}
regrid_arb_path(ap_coord_fn, infiles[0], max_buffer_size_in_kb,
&totals, &weights, vect_size, regrid_range[0], regrid_range[1]);
}
/* else if regridding via a series of input minc file(s) */
else {
for(i = 0; i < n_infiles; i++){
if(verbose){
fprintf(stdout, " | Input file: %s\n", infiles[i]);
}
regrid_minc(infiles[i], max_buffer_size_in_kb,
&totals, &weights, vect_size, regrid_range[0], regrid_range[1]);
}
}
/* initialise min and max counters and divide totals/weights */
num_missed = 0;
min = get_volume_real_value(totals, 0, 0, 0, 0, 0);
max = get_volume_real_value(totals, 0, 0, 0, 0, 0);
w_min = get_volume_real_value(weights, 0, 0, 0, 0, 0);
w_max = get_volume_real_value(weights, 0, 0, 0, 0, 0);
initialize_progress_report(&progress, FALSE, out_inf.nelem[Z_IDX], "Dividing through");
for(i = sizes[perm[0]]; i--;){
for(j = sizes[perm[1]]; j--;){
for(k = sizes[perm[2]]; k--;){
weight = get_volume_real_value(weights, k, j, i, 0, 0);
if(weight < w_min){
w_min = weight;
}
else if(weight > w_max){
w_max = weight;
}
if(weight != 0){
for(v = vect_size; v--;){
value = get_volume_real_value(totals, k, j, i, v, 0) / weight;
if(value < min){
min = value;
}
else if(value > max){
max = value;
}
set_volume_real_value(totals, k, j, i, v, 0, value);
}
}
else {
num_missed++;
}
}
}
update_progress_report(&progress, k + 1);
}
terminate_progress_report(&progress);
/* set the volumes range */
if(verbose){
fprintf(stdout, " + data range: [%g:%g]\n", min, max);
fprintf(stdout, " + weight range: [%g:%g]\n", w_min, w_max);
}
set_volume_real_range(totals, min, max);
set_volume_real_range(weights, w_min, w_max);
if(num_missed > 0 && verbose){
int nvox;
nvox = out_inf.nelem[X_IDX] * out_inf.nelem[Y_IDX] * out_inf.nelem[Z_IDX];
fprintf(stdout,
"\n-regrid_radius possibly too small, no data in %ld/%d[%2.2f%%] voxels\n\n",
num_missed, nvox, ((float)num_missed / nvox * 100));
}
/* rescale data if required */
if(out_range[0] != -DBL_MAX && out_range[1] != DBL_MAX){
double o_min, o_max;
/* get the existing range */
get_volume_real_range(totals, &o_min, &o_max);
/* rescale it */
scale_volume(&totals, o_min, o_max, out_range[0], out_range[1]);
}
/* output the result */
if(verbose){
fprintf(stdout, " | Outputting %s...\n", out_fn);
}
if(output_volume(out_fn, out_dtype, out_is_signed,
0.0, 0.0, totals, history, NULL) != VIO_OK){
fprintf(stderr, "Problems outputing: %s\n\n", out_fn);
}
/* output weights volume if required */
if(weights_fn != NULL){
if(verbose){
fprintf(stdout, " | Outputting %s...\n", weights_fn);
}
if(output_volume(weights_fn, out_dtype, out_is_signed,
0.0, 0.0, weights, history, NULL) != VIO_OK){
fprintf(stderr, "Problems outputting: %s\n\n", weights_fn);
}
}
delete_volume(totals);
delete_volume(weights);
t = current_realtime_seconds();
printf("Total reconstruction time: %ld hours %ld minutes %ld seconds\n", t/3600, (t/60)%60, t%60);
return (EXIT_SUCCESS);
}
/* Main program */
int main(int argc, char *argv[]){
char **infiles, **outfiles;
int nfiles, nout;
char *arg_string;
Loop_Options *loop_options;
char *pname;
int i;
ident_t ident;
scalar_t scalar;
/* Save time stamp and args */
arg_string = time_stamp(argc, argv);
/* Get arguments */
pname = argv[0];
if (ParseArgv(&argc, argv, argTable, 0) || (argc < 2)) {
(void) fprintf(stderr,
"\nUsage: %s [options] [<in1.mnc> ...] <out.mnc>\n",
pname);
(void) fprintf(stderr,
" %s -help\n\n", pname);
exit(EXIT_FAILURE);
}
/* Get output file names */
nout = (Output_list == NULL ? 1 : Output_list_size);
outfiles = malloc(nout * sizeof(*outfiles));
if (Output_list == NULL) {
outfiles[0] = argv[argc-1];
}
else {
for (i=0; i < Output_list_size; i++) {
outfiles[i] = Output_list[i].file;
}
}
/* check for output files */
for (i=0; i < nout; i++){
if(access(outfiles[i], F_OK) == 0 && !clobber){
fprintf(stderr, "%s: %s exists, use -clobber to overwrite\n\n",
argv[0], outfiles[i]);
exit(EXIT_FAILURE);
}
}
/* Get the list of input files either from the command line or
from a file, or report an error if both are specified.
Note that if -outfile is given then there is no output file name
left on argv after option parsing. */
nfiles = argc - 2;
if (Output_list != NULL) nfiles++;
if (filelist == NULL) {
infiles = &argv[1];
}
else if (nfiles <= 0) {
infiles = read_file_names(filelist, &nfiles);
if (infiles == NULL) {
(void) fprintf(stderr,
"Error reading in file names from file \"%s\"\n",
filelist);
exit(EXIT_FAILURE);
}
}
else {
(void) fprintf(stderr,
"Do not specify both -filelist and input file names\n");
exit(EXIT_FAILURE);
}
/* Make sure that we have something to process */
if (nfiles == 0) {
(void) fprintf(stderr, "No input files specified\n");
exit(EXIT_FAILURE);
}
/* Get the expression from the file if needed */
if ((expression == NULL) && (expr_file == NULL)) {
(void) fprintf(stderr,
"An expression must be specified on the command line\n");
exit(EXIT_FAILURE);
}
else if (expression == NULL) {
expression = read_expression_file(expr_file);
}
/* Parse expression argument */
if (debug) fprintf(stderr, "Feeding in expression %s\n", expression);
lex_init(expression);
if (debug) yydebug = 1; else yydebug = 0;
yyparse();
lex_finalize();
/* Optimize the expression tree */
root = optimize(root);
/* Setup the input vector from the input files */
A = new_vector();
for (i=0; i<nfiles; i++) {
if (debug) fprintf(stderr,"Getting file[%d] %s\n", i, argv[i+1]);
scalar = new_scalar(eval_width);
vector_append(A, scalar);
scalar_free(scalar);
}
/* Construct initial symbol table from the A vector. Since setting
a symbol makes a copy, we have to get a handle to that copy. */
rootsym = sym_enter_scope(NULL);
ident = new_ident("A");
sym_set_vector(eval_width, NULL, A, ident, rootsym);
vector_free(A);
A = sym_lookup_vector(ident, rootsym);
if (A==NULL) {
(void) fprintf(stderr, "Error initializing symbol table\n");
exit(EXIT_FAILURE);
}
vector_incr_ref(A);
/* Add output symbols to the table */
if (Output_list == NULL) {
Output_values = NULL;
}
else {
Output_values = malloc(Output_list_size * sizeof(*Output_values));
for (i=0; i < Output_list_size; i++) {
ident = ident_lookup(Output_list[i].symbol);
scalar = new_scalar(eval_width);
sym_set_scalar(eval_width, NULL, scalar, ident, rootsym);
scalar_free(scalar);
Output_values[i] = sym_lookup_scalar(ident, rootsym);
}
}
/* Set default copy_all_header according to number of input files */
if (copy_all_header == DEFAULT_BOOL)
copy_all_header = (nfiles == 1);
if (value_for_illegal_operations == DEFAULT_DBL) {
if (use_nan_for_illegal_values)
value_for_illegal_operations = INVALID_DATA;
else
value_for_illegal_operations = 0.0;
}
/* Do math */
loop_options = create_loop_options();
set_loop_verbose(loop_options, verbose);
set_loop_clobber(loop_options, clobber);
#if MINC2
set_loop_v2format(loop_options, minc2_format);
#endif /* MINC2 */
set_loop_datatype(loop_options, datatype, is_signed,
valid_range[0], valid_range[1]);
set_loop_copy_all_header(loop_options, copy_all_header);
/* only set buffer size if specified */
if(max_buffer_size_in_kb != 0){
set_loop_buffer_size(loop_options, (long) 1024 * max_buffer_size_in_kb);
}
set_loop_check_dim_info(loop_options, check_dim_info);
voxel_loop(nfiles, infiles, nout, outfiles, arg_string, loop_options,
do_math, NULL);
free_loop_options(loop_options);
/* Clean up */
vector_free(A);
sym_leave_scope(rootsym);
if (expr_file != NULL) free(expression);
free(outfiles);
if (Output_list != NULL) free(Output_list);
if (Output_values != NULL) free(Output_values);
exit(EXIT_SUCCESS);
}
int main(int argc, char** argv) {
char *input_path = 0;
char *output_path = 0;
char *dictionary_path = 0;
int force = 0;
int quality = 11;
int decompress = 0;
int repeat = 1;
int verbose = 0;
int lgwin = 0;
clock_t clock_start;
int i;
ParseArgv(argc, argv, &input_path, &output_path, &dictionary_path, &force,
&quality, &decompress, &repeat, &verbose, &lgwin);
clock_start = clock();
for (i = 0; i < repeat; ++i) {
FILE* fin = OpenInputFile(input_path);
FILE* fout = OpenOutputFile(output_path, force || repeat);
int is_ok = 0;
if (decompress) {
is_ok = Decompress(fin, fout, dictionary_path);
} else {
is_ok = Compress(quality, lgwin, fin, fout, dictionary_path);
}
if (!is_ok) {
unlink(output_path);
exit(1);
}
if (fclose(fin) != 0) {
perror("fclose");
exit(1);
}
if (fclose(fout) != 0) {
perror("fclose");
exit(1);
}
}
if (verbose) {
clock_t clock_end = clock();
double duration = (double)(clock_end - clock_start) / CLOCKS_PER_SEC;
int64_t uncompressed_size;
double uncompressed_bytes_in_MB;
if (duration < 1e-9) {
duration = 1e-9;
}
uncompressed_size = FileSize(decompress ? output_path : input_path);
if (uncompressed_size == -1) {
fprintf(stderr, "failed to determine uncompressed file size\n");
exit(1);
}
uncompressed_bytes_in_MB =
(double)(repeat * uncompressed_size) / (1024.0 * 1024.0);
if (decompress) {
printf("Brotli decompression speed: ");
} else {
printf("Brotli compression speed: ");
}
printf("%g MB/s\n", uncompressed_bytes_in_MB / duration);
}
return 0;
}
int main(int argc, char *argv[])
{
VIO_General_transform
transform,
*grid_transform_ptr,
forward_transform;
VIO_Volume
target_vol,
volume;
volume_input_struct
input_info;
VIO_Real
voxel[VIO_MAX_DIMENSIONS],
steps[VIO_MAX_DIMENSIONS],
start[VIO_N_DIMENSIONS],
target_steps[VIO_MAX_DIMENSIONS],
wx,wy,wz, inv_x, inv_y, inv_z,
def_values[VIO_MAX_DIMENSIONS];
static int
clobber_flag = FALSE,
verbose = TRUE,
debug = FALSE;
static char
*target_file;
int
parse_flag,
prog_count,
sizes[VIO_MAX_DIMENSIONS],
target_sizes[VIO_MAX_DIMENSIONS],
xyzv[VIO_MAX_DIMENSIONS],
target_xyzv[VIO_MAX_DIMENSIONS],
index[VIO_MAX_DIMENSIONS],
i,
trans_count;
VIO_progress_struct
progress;
static ArgvInfo argTable[] = {
{"-like", ARGV_STRING, (char *) 0, (char *) &target_file,
"Specify target volume sampling information."},
{"-no_clobber", ARGV_CONSTANT, (char *) FALSE, (char *) &clobber_flag,
"Do not overwrite output file (default)."},
{"-clobber", ARGV_CONSTANT, (char *) TRUE, (char *) &clobber_flag,
"Overwrite output file."},
{"-verbose", ARGV_CONSTANT, (char *) TRUE, (char *) &verbose,
"Write messages indicating progress (default)"},
{"-quiet", ARGV_CONSTANT, (char *) FALSE, (char *) &verbose,
"Do not write log messages"},
{"-debug", ARGV_CONSTANT, (char *) TRUE, (char *) &debug,
"Print out debug info."},
{NULL, ARGV_END, NULL, NULL, NULL}
};
prog_name = argv[0];
target_file = malloc(1024);
strcpy(target_file,"");
/* Call ParseArgv to interpret all command line args (returns TRUE if error) */
parse_flag = ParseArgv(&argc, argv, argTable, 0);
/* Check remaining arguments */
if (parse_flag || argc != 3) print_usage_and_exit(prog_name);
/* Read in file that has a def field to invert */
if (input_transform_file(argv[1], &transform) != OK) {
(void) fprintf(stderr, "%s: Error reading transform file %s\n",
argv[0], argv[1]);
exit(EXIT_FAILURE);
}
for(trans_count=0; trans_count<get_n_concated_transforms(&transform); trans_count++ ) {
grid_transform_ptr = get_nth_general_transform(&transform, trans_count );
if (grid_transform_ptr->type == GRID_TRANSFORM) {
copy_general_transform(grid_transform_ptr,
&forward_transform);
/*
this is the call that should be made
with the latest version of internal_libvolume_io
invert_general_transform(&forward_transform); */
forward_transform.inverse_flag = !(forward_transform.inverse_flag);
volume = grid_transform_ptr->displacement_volume;
if (strlen(target_file)!=0) {
if (debug) print ("Def field will be resampled like %s\n",target_file);
if (!file_exists( target_file ) ) {
(void) fprintf(stderr, "%s: Target file '%s' does not exist\n",
prog_name,target_file);
exit(EXIT_FAILURE);
}
start_volume_input(target_file, 3, (char **)NULL,
NC_UNSPECIFIED, FALSE, 0.0, 0.0,
TRUE, &target_vol,
(minc_input_options *)NULL,
&input_info);
get_volume_XYZV_indices(volume, xyzv);
get_volume_separations (volume, steps);
get_volume_sizes (volume, sizes);
get_volume_XYZV_indices(target_vol, target_xyzv);
get_volume_separations (target_vol, target_steps);
get_volume_sizes (target_vol, target_sizes);
for(i=0; i<VIO_MAX_DIMENSIONS; i++) {
index[i] = 0;
voxel[i] = 0.0;
}
convert_voxel_to_world(target_vol, voxel, &start[VIO_X], &start[VIO_Y], &start[VIO_Z]);
if( volume != (void *) NULL ){
free_volume_data( volume );
}
for(i=VIO_X; i<=VIO_Z; i++) {
steps[ xyzv[i] ] = target_steps[ target_xyzv[i] ] ;
sizes[ xyzv[i] ] = target_sizes[ target_xyzv[i] ] ;
}
set_volume_separations(volume, steps);
set_volume_sizes( volume, sizes);
set_volume_starts(volume, start);
alloc_volume_data( volume );
}
get_volume_sizes(volume, sizes);
get_volume_XYZV_indices(volume,xyzv);
for(i=0; i<VIO_MAX_DIMENSIONS; i++){
index[i] = 0;
}
if (verbose){
initialize_progress_report(&progress, FALSE,
sizes[xyzv[VIO_X]]*sizes[xyzv[VIO_Y]]*sizes[xyzv[VIO_Z]]+1,
"Inverting def field");
}
prog_count = 0;
for(index[xyzv[VIO_X]]=0; index[xyzv[VIO_X]]<sizes[xyzv[VIO_X]]; index[xyzv[VIO_X]]++)
for(index[xyzv[VIO_Y]]=0; index[xyzv[VIO_Y]]<sizes[xyzv[VIO_Y]]; index[xyzv[VIO_Y]]++)
for(index[xyzv[VIO_Z]]=0; index[xyzv[VIO_Z]]<sizes[xyzv[VIO_Z]]; index[xyzv[VIO_Z]]++) {
index[ xyzv[VIO_Z+1] ] = 0;
for(i=0; i<VIO_MAX_DIMENSIONS; i++) voxel[i] = (VIO_Real)index[i];
convert_voxel_to_world(volume, voxel, &wx, &wy, &wz);
if (sizes[ xyzv[VIO_Z] ] ==1)
general_inverse_transform_point_in_trans_plane(&forward_transform,
wx, wy, wz,
&inv_x, &inv_y, &inv_z);
else
grid_inverse_transform_point(&forward_transform,
wx, wy, wz,
&inv_x, &inv_y, &inv_z);
def_values[VIO_X] = inv_x - wx;
def_values[VIO_Y] = inv_y - wy;
def_values[VIO_Z] = inv_z - wz;
for(index[xyzv[VIO_Z+1]]=0; index[xyzv[VIO_Z+1]]<3; index[xyzv[VIO_Z+1]]++)
set_volume_real_value(volume,
index[0],index[1],index[2],index[3],index[4],
def_values[ index[ xyzv[VIO_Z+1] ]]);
prog_count++;
if (verbose)
update_progress_report(&progress, prog_count);
}
if (verbose)
terminate_progress_report(&progress);
delete_general_transform(&forward_transform);
grid_transform_ptr->inverse_flag = !(grid_transform_ptr->inverse_flag);
}
}
/* Write out the transform */
if (output_transform_file(argv[2], NULL, &transform) != OK) {
(void) fprintf(stderr, "%s: Error writing transform file %s\n",
argv[0], argv[2]);
exit(EXIT_FAILURE);
}
exit(EXIT_SUCCESS);
}
int main(int argc, char *argv[])
{
char *infile, *outfile;
char *arg_string;
int inmincid;
int input_vector_length;
int ivalue;
Loop_Options *loop_options;
Program_Data program_data;
/* Save time stamp and args */
arg_string = time_stamp(argc, argv);
/* Get arguments */
if (ParseArgv(&argc, argv, argTable, 0) || (argc != 3)) {
(void) fprintf(stderr, "\nUsage: %s [options] <in.mnc> <out.mnc>\n",
argv[0]);
(void) fprintf(stderr, " %s -help\n\n",
argv[0]);
exit(EXIT_FAILURE);
}
infile = argv[1];
outfile = argv[2];
/* Check for conflicting options */
if ((conversion_type != CONV_DEFAULT) &&
(linear_coefficients.numvalues > 0)) {
(void) fprintf(stderr,
"Do not specify -linear with other conversion options\n");
exit(EXIT_FAILURE);
}
/* Set up conversion information */
if (conversion_type == CONV_DEFAULT) conversion_type = CONV_MAGNITUDE;
program_data.conversion_type = conversion_type;
program_data.num_coefficients = 0;
program_data.linear_coefficients = NULL;
/* Check for coefficients for linear combination */
if (linear_coefficients.numvalues > 0) {
conversion_type = CONV_LINEAR;
program_data.conversion_type = conversion_type;
program_data.num_coefficients = linear_coefficients.numvalues;
program_data.linear_coefficients =
malloc(linear_coefficients.numvalues *
sizeof(*program_data.linear_coefficients));
for (ivalue=0; ivalue < linear_coefficients.numvalues; ivalue++) {
program_data.linear_coefficients[ivalue] =
linear_coefficients.values[ivalue];
}
}
/* Open the input file and get the vector length */
inmincid = miopen(infile, NC_NOWRITE);
input_vector_length = get_vector_length(inmincid);
if (input_vector_length < 0) {
fprintf(stderr, str_wrong_dimension_order);
exit(EXIT_FAILURE);
}
if (input_vector_length < 1) input_vector_length = 1;
/* Check that this length is okay */
if ((conversion_type == CONV_GREY) &&
(input_vector_length != 3) && (input_vector_length > 1)) {
(void) fprintf(stderr, "Input file does not contain RGB data\n");
exit(EXIT_FAILURE);
}
if ((conversion_type == CONV_LINEAR) &&
(input_vector_length != program_data.num_coefficients) &&
(input_vector_length > 1)) {
(void) fprintf(stderr,
"Input vector length does not match number of linear coefficients\n");
exit(EXIT_FAILURE);
}
/* Set up looping options */
loop_options = create_loop_options();
set_loop_clobber(loop_options, clobber);
set_loop_verbose(loop_options, verbose);
#if MINC2
set_loop_v2format(loop_options, v2format);
#endif /* MINC2 */
set_loop_datatype(loop_options, datatype, is_signed,
valid_range[0], valid_range[1]);
set_loop_output_vector_size(loop_options, 1);
set_loop_buffer_size(loop_options, (long) buffer_size * 1024);
set_loop_first_input_mincid(loop_options, inmincid);
/* Do loop */
voxel_loop(1, &infile, 1, &outfile, arg_string, loop_options,
do_makescalar, (void *) &program_data);
/* Free stuff */
if (program_data.linear_coefficients != NULL) {
free(program_data.linear_coefficients);
}
if (linear_coefficients.values != NULL) {
free(linear_coefficients.values);
}
exit(EXIT_SUCCESS);
}
int
main(int argc, char *argv[])
{
int ifile;
Acr_Group group_list;
char **file_list; /* List of file names */
Data_Object_Info **file_info_list;
int num_file_args; /* Number of files on command line */
int num_files; /* Total number of files */
string_t out_dir; /* Output directory */
string_t message; /* Generic message */
int num_files_ok; /* Actual number of DICOM/IMA files */
struct stat st;
int length;
int exit_status;
G.mosaic_seq = MOSAIC_SEQ_UNKNOWN; /* Assume ascending by default. */
G.splitDynScan = FALSE; /* Don't split dynamic scans by default */
G.splitEcho = TRUE; /* Do split by echo by default */
G.use_stdin = FALSE; /* Do not read file list from stdin */
G.filename_format = NULL;
G.dirname_format = NULL;
G.minc_history = time_stamp(argc, argv); /* Create minc history string */
G.prefer_coords = FALSE;
G.abort_on_error = FALSE;
G.pname = argv[0]; /* get program name */
/* Get the input parameters and file names.
*/
if (ParseArgv(&argc, argv, argTable, 0)) {
usage();
}
if (argc < 2) {
usage();
}
if (G.List) {
num_file_args = argc - 1; /* Assume no directory given. */
}
else {
num_file_args = argc - 2; /* Assume last arg is directory. */
strcpy(out_dir, argv[argc - 1]);
/* make sure path ends with slash
*/
length = strlen(out_dir);
if (out_dir[length - 1] != '/') {
out_dir[length++] = '/';
out_dir[length++] = '\0';
}
if (stat(out_dir, &st) != 0 || !S_ISDIR(st.st_mode)) {
fprintf(stderr, "The final argument, '%s', is not a directory\n",
out_dir);
exit(EXIT_FAILURE);
}
}
/* Get space for file lists */
/* Allocate the array of pointers used to implement the
* list of filenames.
*/
file_list = malloc(1 * sizeof(char *));
CHKMEM(file_list);
/* Go through the list of files, expanding directories where they
* are encountered...
*/
num_files = 0;
for (ifile = 0 ; ifile < num_file_args; ifile++) {
#if HAVE_DIRENT_H
if (stat(argv[ifile + 1], &st) == 0 && S_ISDIR(st.st_mode)) {
DIR *dp;
struct dirent *np;
char *tmp_str;
if (G.Debug) {
printf("Expanding directory '%s'\n", argv[ifile + 1]);
}
length = strlen(argv[ifile + 1]);
dp = opendir(argv[ifile + 1]);
if (dp != NULL) {
while ((np = readdir(dp)) != NULL) {
/* Generate the full path to the file.
*/
tmp_str = malloc(length + strlen(np->d_name) + 2);
strcpy(tmp_str, argv[ifile + 1]);
if (tmp_str[length-1] != '/') {
tmp_str[length] = '/';
tmp_str[length+1] = '\0';
}
strcat(&tmp_str[length], np->d_name);
if (stat(tmp_str, &st) == 0 && S_ISREG(st.st_mode)) {
file_list = realloc(file_list,
(num_files + 1) * sizeof(char *));
file_list[num_files++] = tmp_str;
}
else {
free(tmp_str);
}
}
closedir(dp);
}
else {
fprintf(stderr, "Error opening directory '%s'\n",
argv[ifile + 1]);
}
}
else {
file_list = realloc(file_list, (num_files + 1) * sizeof(char *));
file_list[num_files++] = strdup(argv[ifile + 1]);
}
#else
file_list = realloc(file_list, (num_files + 1) * sizeof(char *));
file_list[num_files++] = strdup(argv[ifile + 1]);
#endif
}
if (G.use_stdin) {
char linebuf[1024];
char *p;
while (fgets(linebuf, sizeof(linebuf), stdin) != NULL) {
/* Strip off newline at end of string.
*/
for (p = linebuf; *p != '\0'; p++) {
if (*p == '\n') {
*p = '\0';
}
}
if (strlen(linebuf) != 0) {
file_list = realloc(file_list,
(num_files + 1) * sizeof(char *));
file_list[num_files++] = strdup(linebuf);
}
}
}
file_info_list = malloc(num_files * sizeof(*file_info_list));
CHKMEM(file_info_list);
/* figure out what kind of files we have -
* supported types are:
*
* IMA (Siemens .ima format - Numaris 3.5)
* N4DCM (Siemens DICOM - Numaris 4)
*
* if not all same type, return an error
*
* we start by assuming N4DCM with no offset - we find that the
* file is IMA or has an offset (the 128 byte + DICM offset seen
* on Syngo CD's and exports) then the appropriate flag will be
* set.
*/
printf("Checking file types...\n");
if (check_file_type_consistency(num_files, file_list) < 0) {
exit(EXIT_FAILURE);
}
/* Now loop over all files, getting basic info on each
*/
num_files_ok = 0;
for (ifile = 0; ifile < num_files; ifile++) {
char *cur_fname_ptr = file_list[ifile];
if (!G.Debug) {
sprintf(message, "Parsing %d files", num_files);
progress(ifile, num_files, message);
}
if (G.file_type == IMA) {
group_list = siemens_to_dicom(cur_fname_ptr, ACR_IMAGE_GID - 1);
}
else {
/* read up to but not including pixel data
*/
group_list = read_numa4_dicom(cur_fname_ptr, ACR_IMAGE_GID - 1);
}
if (group_list == NULL) {
/* This file appears to be invalid - it is probably a dicomdir
* file or some other stray junk in the directory.
*/
printf("Skipping file %s, which is not in the expected format.\n",
cur_fname_ptr);
free(cur_fname_ptr);
}
else {
/* Copy it back to the (possibly earlier) position in the real
* file list.
*/
file_list[num_files_ok] = cur_fname_ptr;
/* allocate space for the current entry to file_info_list
*/
file_info_list[num_files_ok] = malloc(sizeof(*file_info_list[0]));
CHKMEM(file_info_list[num_files_ok]);
file_info_list[num_files_ok]->file_index = num_files_ok;
parse_dicom_groups(group_list, file_info_list[num_files_ok]);
/* put the file name into the info list
*/
file_info_list[num_files_ok]->file_name = strdup(file_list[num_files_ok]);
/* Delete the group list now that we're done with it
*/
acr_delete_group_list(group_list);
num_files_ok++;
}
} /* end of loop over files to get basic info */
if (G.Debug) {
printf("Using %d files\n", num_files_ok);
}
num_files = num_files_ok;
printf("Sorting %d files... ", num_files);
/* sort the files into series based on acquisition number
*/
qsort(file_info_list, num_files, sizeof(file_info_list[0]),
dcm_sort_function);
/* If DEBUG, print a list of all files.
*/
if (G.Debug) {
printf("\n");
for (ifile = 0; ifile < num_files; ifile++) {
Data_Object_Info *info = file_info_list[ifile];
char *fname;
if ((ifile % 16) == 0) {
printf("%-4s %-32.32s %-14s %-8s %-8s %-4s %-4s %-4s %-4s %-4s %-4s %-4s %-4s %-4s %-5s %-16s\n",
"num",
"filename",
"studyid",
"serialno",
"acq",
"nec",
"iec",
"ndy",
"idy",
"nsl",
"isl",
"acol",
"rcol",
"mrow",
"img#",
"seq");
}
/* Print out info about file. Truncate the name if necessary.
*/
fname = info->file_name;
if (strlen(fname) > 32) {
fname += strlen(fname) - 32;
}
printf("%4d %-32.32s %14.6f %8d %8d %4d %4d %4d %4d %4d %4d %4d %4d %4d %5d %-16s\n",
ifile,
fname,
info->study_id,
info->scanner_serialno,
info->acq_id,
info->num_echoes,
info->echo_number,
info->num_dyn_scans,
info->dyn_scan_number,
info->num_slices_nominal,
info->slice_number,
info->acq_cols,
info->rec_cols,
info->num_mosaic_rows,
info->global_image_number,
info->sequence_name);
}
}
printf("Done sorting files.\n");
/* Loop over files, processing by acquisition */
if (G.List) {
printf("Listing files by series...\n");
}
else {
printf("Processing files, one series at a time...\n");
}
exit_status = use_the_files(num_files, file_info_list, out_dir);
if (G.List) {
printf("Done listing files.\n");
}
else {
printf("Done processing files.\n");
}
free_list(num_files, file_list, file_info_list);
free(file_list);
free(file_info_list);
exit(exit_status);
}
int main(int argc, char *argv[])
{
char *pname;
char *filename, *tempfile, *newfile;
char string[1024];
char *variable_name, *attribute_name;
int created_tempfile;
int done_redef;
int iatt;
int mincid, varid;
int variable_exists, attribute_exists;
nc_type attribute_type, new_type;
int attribute_length, new_length;
void *new_value;
int total_length, alloc_length, ival;
char *zeros;
int old_ncopts;
/* Parse the command line */
pname=argv[0];
if (ParseArgv(&argc, argv, argTable, 0) || (argc != 2)) {
(void) fprintf(stderr, "\nUsage: %s [<options>] <file.mnc>\n",
pname);
(void) fprintf(stderr, " %s [-help]\n\n", pname);
exit(EXIT_FAILURE);
}
filename = argv[1];
/* Create temp file name. First try looking for minc extension, then
a compression extension. Chop off the unwanted extension. */
(void) strncpy(string, filename, sizeof(string)-1);
tempfile = strstr(string, MINC_EXTENSION);
if (tempfile != NULL) {
tempfile += strlen(MINC_EXTENSION);
if (*tempfile == '\0')
tempfile = NULL;
}
else {
tempfile = strstr(string, GZIP_EXTENSION);
if (tempfile == NULL)
tempfile = strstr(string, BZIP_EXTENSION);
if (tempfile == NULL)
tempfile = strstr(string, BZIP2_EXTENSION);
if (tempfile == NULL)
tempfile = strstr(string, COMPRESS_EXTENSION);
if (tempfile == NULL)
tempfile = strstr(string, PACK_EXTENSION);
if (tempfile == NULL)
tempfile = strstr(string, ZIP_EXTENSION);
}
if (tempfile != NULL) {
*tempfile = '\0';
tempfile = string;
}
/* If tempfile == NULL, then either we have a minc file or we don't know
how to edit the file in place. Check that it is a minc file. */
if (tempfile == NULL) {
newfile = miexpand_file(filename, tempfile, TRUE, &created_tempfile);
if (created_tempfile) {
if (newfile != NULL) {
(void) remove(newfile);
free(newfile);
}
(void) fprintf(stderr, "Cannot edit file \"%s\" in place.\n",
filename);
exit(EXIT_FAILURE);
}
}
/* Expand the file. */
newfile = miexpand_file(filename, tempfile, FALSE, &created_tempfile);
if (newfile == NULL) {
(void) fprintf(stderr, "Error decompressing file \"%s\"\n",
filename);
exit(EXIT_FAILURE);
}
/* If a new file was created, get rid of the old one */
if (created_tempfile) {
(void) remove(filename);
}
/* Open the file */
mincid = miopen(newfile, NC_WRITE);
/* Loop through attribute list, modifying values */
done_redef = FALSE;
ncopts = NC_VERBOSE;
zeros = NULL;
alloc_length = 0;
for (iatt=0; iatt < attribute_list_size; iatt++) {
/* Get variable and attribute name */
variable_name = attribute_list[iatt].variable;
attribute_name = attribute_list[iatt].attribute;
/* Check for attribute existence */
if (strlen(variable_name) == 0) {
varid = NC_GLOBAL;
variable_exists = TRUE;
}
else {
old_ncopts = ncopts; ncopts = 0;
varid = ncvarid(mincid, variable_name);
ncopts = old_ncopts;
variable_exists = (varid != MI_ERROR);
}
attribute_type = NC_CHAR;
attribute_length = 0;
if (variable_exists) {
old_ncopts = ncopts; ncopts = 0;
attribute_exists =
(ncattinq(mincid, varid, attribute_name,
&attribute_type, &attribute_length) != MI_ERROR);
ncopts = old_ncopts;
}
else
attribute_exists = FALSE;
/* Are we inserting or deleting? */
switch (attribute_list[iatt].action) {
case Insert_attribute:
case Append_attribute:
if (attribute_list[iatt].value != NULL) {
new_type = NC_CHAR;
new_length = strlen(attribute_list[iatt].value)+1;
new_value = (void *) attribute_list[iatt].value;
}
else {
new_type = NC_DOUBLE;
new_length = attribute_list[iatt].num_doubles;
new_value = (void *) attribute_list[iatt].double_values;
}
/* For append we have to copy the entire attribute, if it
* already exists.
*/
if (attribute_list[iatt].action == Append_attribute &&
attribute_exists) {
char *tmp_value;
/* Verify that the existing type matches the newly
* requested type. Don't allow a -dappend on a
* string attribute, for example.
*/
if (new_type != attribute_type) {
fprintf(stderr,
"Can't append %s data to %s attribute %s:%s.\n",
(new_type == NC_DOUBLE) ? "double" : "string",
(attribute_type == NC_DOUBLE) ? "double" : "string",
variable_name, attribute_name);
exit(EXIT_FAILURE);
}
new_type = attribute_type;
tmp_value = malloc((attribute_length + new_length) * nctypelen(new_type));
ncattget(mincid, varid, attribute_name, tmp_value);
/* For string attributes, remove any trailing null
* character before appending.
*/
if (new_type == NC_CHAR && tmp_value[attribute_length-1] == 0) {
attribute_length--;
}
memcpy(tmp_value + attribute_length * nctypelen(new_type),
new_value,
new_length * nctypelen(new_type));
new_length += attribute_length;
new_value = (void *) tmp_value;
}
total_length = attribute_length*nctypelen(attribute_type);
if (!attribute_exists ||
(total_length < new_length*nctypelen(new_type))) {
if (! done_redef) {
done_redef = TRUE;
(void) ncredef(mincid);
}
}
else if (!done_redef && attribute_exists && (total_length > 0)) {
if (total_length > alloc_length) {
if (zeros != NULL) free(zeros);
zeros = malloc(total_length);
alloc_length = total_length;
for (ival=0; ival < alloc_length; ival++)
zeros[ival] = '\0';
}
(void) ncattput(mincid, varid, attribute_name, NC_CHAR,
total_length, zeros);
(void) ncsync(mincid);
}
if (!variable_exists) {
old_ncopts = ncopts; ncopts = 0;
varid = micreate_group_variable(mincid, variable_name);
ncopts = old_ncopts;
if (varid == MI_ERROR) {
varid = ncvardef(mincid, variable_name, NC_INT,
0, NULL);
}
variable_exists = (varid != MI_ERROR);
}
if (variable_exists) {
(void) ncattput(mincid, varid, attribute_name,
new_type, new_length, new_value);
}
break;
case Delete_attribute:
if (attribute_exists) {
if (! done_redef) {
done_redef = TRUE;
(void) ncredef(mincid);
}
(void) ncattdel(mincid, varid, attribute_name);
}
break;
default:
(void) fprintf(stderr, "Program error: unknown action %d\n",
(int) attribute_list[iatt].action);
exit(EXIT_FAILURE);
}
}
ncopts = NC_VERBOSE | NC_FATAL;
/* Close the file */
(void) miclose(mincid);
/* Free stuff */
free(newfile);
if (zeros != NULL) free(zeros);
exit(EXIT_SUCCESS);
}
int main(int argc, char **argv)
{
int c, i;
Coord_list coord_buf;
char *coord_fn;
int buff_size = 2048;
int prev_size;
/* Get arguments */
if(ParseArgv(&argc, argv, argTable, 0)) {
(void)fprintf(stderr, "\nUsage: %s [options] <coords.cfg>\n", argv[0]);
(void)fprintf(stderr, " %s -help\n\n", argv[0]);
exit(EXIT_FAILURE);
}
coord_fn = argv[1];
/* initialise the parser with the config file */
fprintf(stderr, "Opening coord-file %s\n", coord_fn);
if(!init_arb_path(coord_fn, NULL)) {
fprintf(stderr, "Failed to init arb_path, this isn't good\n");
}
/* suck in all the co-ordinates (brough-ha ha ha!) */
coord_buf = get_some_arb_path_coords(buff_size);
while (coord_buf->n_pts != 0) {
/* allocate some memory */
prev_size = n_coords;
n_coords += coord_buf->n_pts;
x_coord = (double *)realloc(x_coord, n_coords * sizeof(double));
y_coord = (double *)realloc(y_coord, n_coords * sizeof(double));
z_coord = (double *)realloc(z_coord, n_coords * sizeof(double));
/* add the current list */
for(c = 0; c < coord_buf->n_pts; c++) {
x_coord[prev_size + c] = coord_buf->pts[c].coord[0];
y_coord[prev_size + c] = coord_buf->pts[c].coord[1];
z_coord[prev_size + c] = coord_buf->pts[c].coord[2];
/* set min and max */
for(i = 3; i--;) {
if(coord_buf->pts[c].coord[i] > max[i]) {
max[i] = coord_buf->pts[c].coord[i];
}
if(coord_buf->pts[c].coord[i] < min[i]) {
min[i] = coord_buf->pts[c].coord[i];
}
}
}
fprintf(stdout, "Got %d co-ords, realloced to %d points\n", coord_buf->n_pts,
n_coords);
/* get the next lot of co-ordinates */
coord_buf = get_some_arb_path_coords(buff_size);
}
fprintf(stdout, "Got %d coords\n", n_coords);
fprintf(stdout, "Min [%g:%g:%g] Max [%g:%g:%g]\n", min[0], min[1], min[2], max[0],
max[1], max[2]);
/* init the quat */
trackball(curquat, 0.0, 0.0, 0.0, 0.0);
/* GLUT stuff */
glutInit(&argc, argv);
glutInitDisplayMode(GLUT_DOUBLE | GLUT_RGB | GLUT_DEPTH);
glutCreateWindow("regrid viewer");
glutDisplayFunc(mainDisplay);
glutReshapeFunc(mainReshape);
glutVisibilityFunc(vis);
glutMouseFunc(mouse);
glutMotionFunc(motion);
glutKeyboardFunc(KeyPressed);
glutSpecialFunc(SpecialKey);
glMatrixMode(GL_PROJECTION);
gluPerspective( /* field of view in degree */ 40.0,
/* aspect ratio */ 1.0,
/* Z near */ 1.0, /* Z far */ 40.0);
glMatrixMode(GL_MODELVIEW);
gluLookAt(0.0, 0.0, 30.0, /* eye is at (0,0,30) */
0.0, 0.0, 0.0, /* center is at (0,0,0) */
0.0, 1.0, 0.); /* up is in positive Y direction */
glPushMatrix(); /* dummy push so we can pop on model
recalc */
glutMainLoop();
return TRUE;
}
int main(int argc, char *argv[])
{
char *pname, *tagfile1, *tagfile2, *outtag, *history;
Real **tags1, **tags2, **new_tags, *this_tag;
int n_volumes1, n_volumes2, n_tag_points1, n_tag_points2;
int ipoint1, ipoint2, icoord, near_tag;
STRING *labels1, *labels2, *new_labels, this_label;
double min_distsq, distsq, diff, maximum_distsq;
size_t string_length;
FILE *fp;
char dist_string[64];
/* Save history */
history = time_stamp(argc, argv);
/* Parse arguments */
pname = argv[0];
if (ParseArgv(&argc, argv, argTable, 0) || (argc != 4)) {
(void) fprintf(stderr,
"\nUsage: %s [<options>] infile1.tag file2.tag outfile2.tag\n\n",
pname);
exit(EXIT_FAILURE);
}
tagfile1 = argv[1];
tagfile2 = argv[2];
outtag = argv[3];
maximum_distsq = maximum_distance * maximum_distance;
/* Read in first tag file */
if ((open_file_with_default_suffix(tagfile1,
get_default_tag_file_suffix(),
READ_FILE, ASCII_FORMAT, &fp) != OK) ||
(input_tag_points(fp, &n_volumes1, &n_tag_points1,
&tags1, NULL,
NULL, NULL, NULL, &labels1) != OK)) {
(void) fprintf(stderr, "%s: Error reading tag file %s\n",
pname, tagfile1);
exit(EXIT_FAILURE);
}
(void) close_file(fp);
/* Read in second tag file */
if ((open_file_with_default_suffix(tagfile2,
get_default_tag_file_suffix(),
READ_FILE, ASCII_FORMAT, &fp) != OK) ||
(input_tag_points(fp, &n_volumes2, &n_tag_points2,
&tags2, NULL,
NULL, NULL, NULL, &labels2) != OK)) {
(void) fprintf(stderr, "%s: Error reading tag file %s\n",
pname, tagfile2);
exit(EXIT_FAILURE);
}
(void) close_file(fp);
/* Allocate space for output tags */
new_tags = MALLOC(n_tag_points1 * sizeof(*new_tags));
new_labels = MALLOC(n_tag_points1 * sizeof(*new_labels));
/* Loop through tags in first file */
for (ipoint1=0; ipoint1 < n_tag_points1; ipoint1++) {
/* Look for nearest tag in second file */
min_distsq = 0.0;
for (ipoint2=0; ipoint2 < n_tag_points2; ipoint2++) {
/* Calculate distance-squared */
distsq = 0;
for (icoord=0; icoord < WORLD_NDIMS; icoord++) {
diff = tags1[ipoint1][icoord] - tags2[ipoint2][icoord];
distsq += diff * diff;
}
/* Check if this is the minimum */
if ((ipoint2 == 0) || (min_distsq > distsq)) {
near_tag = ipoint2;
min_distsq = distsq;
}
}
/* Save the nearest tag */
if (min_distsq <= maximum_distsq) {
this_tag = tags2[near_tag];
this_label = labels2[near_tag];
}
else {
this_tag = tags1[ipoint1];
this_label = "not found";
}
(void) sprintf(dist_string, " (%.2f mm)", sqrt(min_distsq));
new_tags[ipoint1] = this_tag;
string_length = strlen(labels1[ipoint1]) + strlen(this_label) +
strlen(SEP_STRING) + strlen(dist_string) + 1;
new_labels[ipoint1] = MALLOC(string_length);
(void) strcpy(new_labels[ipoint1], labels1[ipoint1]);
(void) strcat(new_labels[ipoint1], SEP_STRING);
(void) strcat(new_labels[ipoint1], this_label);
(void) strcat(new_labels[ipoint1], dist_string);
}
if (output_tag_file(outtag, history, 2, n_tag_points1,
tags1, new_tags,
NULL, NULL, NULL, new_labels) != OK) {
(void) fprintf(stderr, "Error writing out labels\n");
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
int main(int argc, char *argv[])
{
char *filename;
int mincid, imgid, icvid, ndims, dims[MAX_VAR_DIMS];
nc_type datatype;
int is_signed;
long start[MAX_VAR_DIMS], count[MAX_VAR_DIMS], end[MAX_VAR_DIMS];
long size;
int idim;
void *data;
double temp;
/* Check arguments */
if (ParseArgv(&argc, argv, argTable, 0) || (argc != 2)) {
(void) fprintf(stderr, "\nUsage: %s [<options>] <mincfile>\n", argv[0]);
(void) fprintf(stderr, " %s -help\n\n", argv[0]);
exit(EXIT_FAILURE);
}
filename = argv[1];
/* Check that a normalization option was specified */
if (normalize_output == VIO_BOOL_DEFAULT) {
(void) fprintf(stderr,
"Please specify either -normalize or -nonormalize\n");
(void) fprintf(stderr, "Usually -normalize is most appropriate\n");
exit(EXIT_FAILURE);
}
/* Open the file */
mincid = miopen(filename, NC_NOWRITE);
/* Inquire about the image variable */
imgid = ncvarid(mincid, MIimage);
(void) ncvarinq(mincid, imgid, NULL, NULL, &ndims, dims, NULL);
(void)miget_datatype(mincid, imgid, &datatype, &is_signed);
/* Check if arguments set */
/* Get output data type */
if (output_datatype == INT_MAX) output_datatype = datatype;
/* Get output sign */
if (output_signed == INT_MAX) {
if (output_datatype == datatype)
output_signed = is_signed;
else
output_signed = (output_datatype != NC_BYTE);
}
/* Get output range */
if (valid_range[0] == DBL_MAX) {
if ((output_datatype == datatype) && (output_signed == is_signed)) {
(void) miget_valid_range(mincid, imgid, valid_range);
}
else {
(void) miget_default_range(output_datatype, output_signed,
valid_range);
}
}
if (valid_range[0] > valid_range[1]) {
temp = valid_range[0];
valid_range[0] = valid_range[1];
valid_range[1] = temp;
}
/* Set up image conversion */
icvid = miicv_create();
(void) miicv_setint(icvid, MI_ICV_TYPE, output_datatype);
(void) miicv_setstr(icvid, MI_ICV_SIGN, (output_signed ?
MI_SIGNED : MI_UNSIGNED));
(void) miicv_setdbl(icvid, MI_ICV_VALID_MIN, valid_range[0]);
(void) miicv_setdbl(icvid, MI_ICV_VALID_MAX, valid_range[1]);
if ((output_datatype == NC_FLOAT) || (output_datatype == NC_DOUBLE)) {
(void) miicv_setint(icvid, MI_ICV_DO_NORM, TRUE);
(void) miicv_setint(icvid, MI_ICV_USER_NORM, TRUE);
}
else if (normalize_output) {
(void) miicv_setint(icvid, MI_ICV_DO_NORM, TRUE);
}
(void) miicv_attach(icvid, mincid, imgid);
/* Set input file start, count and end vectors for reading a slice
at a time */
for (idim=0; idim < ndims; idim++) {
(void) ncdiminq(mincid, dims[idim], NULL, &end[idim]);
}
(void) miset_coords(ndims, (long) 0, start);
(void) miset_coords(ndims, (long) 1, count);
size = nctypelen(output_datatype);
for (idim=ndims-2; idim < ndims; idim++) {
count[idim] = end[idim];
size *= count[idim];
}
/* Allocate space */
data = malloc(size);
/* Loop over input slices */
while (start[0] < end[0]) {
/* Read in the slice */
(void) miicv_get(icvid, start, count, data);
/* Write out the slice */
if (fwrite(data, sizeof(char), (size_t) size, stdout) != size) {
(void) fprintf(stderr, "Error writing data.\n");
exit(EXIT_FAILURE);
}
/* Increment start counter */
idim = ndims-1;
start[idim] += count[idim];
while ( (idim>0) && (start[idim] >= end[idim])) {
start[idim] = 0;
idim--;
start[idim] += count[idim];
}
} /* End loop over slices */
/* Clean up */
(void) miclose(mincid);
(void) miicv_free(icvid);
free(data);
exit(EXIT_SUCCESS);
}
int
waste_main_start(int argc, char **argv)
{
SetProgramDirectory(argv[0]);
g_log_level=ds_Console;
//g_log_level=ds_Debug;
_logfile=stderr;
installsighandler();
log_printf(ds_Console,"%s starting up...",g_nameverstr);
MYSRAND();
#ifdef _DEFINE_WXUI
extern void ParseArgv (const char *, bool);
int i;
for (i = 1; i < argc; i++) {
ParseArgv(argv[i], true);
}
extern int g_opt_forceProfileDlg;
if (Prefs_SelectProfile(g_opt_forceProfileDlg)) return 1;
strcat(g_config_prefix,g_profile_name);
#else
strcat(g_config_prefix,"default");
#endif
if (!g_exit) //emergency break!
{
#ifdef _WIN32
WSADATA wsaData;
if (WSAStartup(MAKEWORD(2, 0), &wsaData)) {
memset(&g_key,0,sizeof(g_key));
MessageBox(NULL,"Error initializing Winsock\n",APP_NAME " Error",0);
return 1;
}
#endif
UnifiedReadConfig();
InitialLoadDb();
PrepareDownloadDirectory();
int need_setup=0;
#ifndef _DEFINE_SRV
need_setup=g_config->ReadInt(CONFIG_valid,0)<5;
if (need_setup) {
#ifdef _DEFINE_WXUI
::wxMessageBox(_T("This is your first time running WASTE.\n"
"Please open the 'Preferences' window and press\n"
"'Generate a new private key...', so that you can\n"
"join and use the WASTE network."),
_T("Welcome to WASTE"),
wxICON_HAND|wxOK);
g_config->WriteInt(CONFIG_valid,5);
g_config->Flush();
#else
if (!DialogBox(hInstance,MAKEINTRESOURCE(IDD_SETUPWIZ),NULL,SetupWi
zProc)) {
delete g_config;
memset(&g_key,0,sizeof(g_key));
return 1;
};
g_config->WriteInt(CONFIG_valid,5);
g_config->Flush();
#endif
};
#endif /* _DEFINE_SRV */
if (!g_key.bits && !need_setup) {
reloadKey(
g_config->ReadInt(CONFIG_storepass,CONFIG_storepass_DEFAULT)?
g_config->ReadString(CONFIG_keypass,CONFIG_keypass_DEFAULT):
NULL
);
};
InitializeNetworkparts();
#ifdef _DEFINE_WXUI
int x;
for (x = 0; x < SEARCHCACHE_NUMITEMS; x ++) g_searchcache[x]=new SearchCacheItem;
#endif
#ifndef _DEFINE_SRV
extern char *g_opt_wasteOpen;
if (g_opt_wasteOpen) {
handleWasteURL(g_opt_wasteOpen);
free(g_opt_wasteOpen);
g_opt_wasteOpen = NULL;
};
#endif /* _DEFINE_SRV */
}
return (g_exit);
}
int main(int argc, char *argv[])
{
char **infiles, *outfiles[3];
int nfiles, nout;
char *arg_string;
Norm_Data norm_data;
Average_Data average_data;
Loop_Options *loop_options;
double *vol_mean, vol_total, nvols, global_mean, total_weight;
int ifile, iweight;
int weights_specified;
int first_mincid, dimid, varid, dim[MAX_VAR_DIMS];
int ndims;
long start, count;
int old_ncopts;
int strlength;
char dimname[MAX_NC_NAME];
/* Save time stamp and args */
arg_string = time_stamp(argc, argv);
/* Get arguments */
if (ParseArgv(&argc, argv, argTable, 0) || (argc < 2)) {
(void) fprintf(stderr,
"\nUsage: %s [options] [<in1.mnc> ...] <out.mnc>\n",
argv[0]);
(void) fprintf(stderr,
" %s -help\n\n", argv[0]);
exit(EXIT_FAILURE);
}
outfiles[0] = outfiles[1] = outfiles[2] = NULL;
outfiles[0] = argv[argc-1];
nout = 1;
if( sdfile != NULL )
outfiles[nout++] = sdfile;
if( weightfile != NULL )
outfiles[nout++] = weightfile;
first_mincid = MI_ERROR;
/* Get the list of input files either from the command line or
from a file, or report an error if both are specified */
nfiles = argc - 2;
if (filelist == NULL) {
infiles = &argv[1];
}
else if (nfiles <= 0) {
infiles = read_file_names(filelist, &nfiles);
if (infiles == NULL) {
(void) fprintf(stderr,
"Error reading in file names from file \"%s\"\n",
filelist);
exit(EXIT_FAILURE);
}
}
else {
(void) fprintf(stderr,
"Do not specify both -filelist and input file names\n");
exit(EXIT_FAILURE);
}
/* Make sure that we have something to process */
if (nfiles == 0) {
(void) fprintf(stderr, "No input files specified\n");
exit(EXIT_FAILURE);
}
/* Set default value of copy_all_header */
if (copy_all_header == DEFAULT_BOOLEAN) {
copy_all_header = (nfiles <= 1);
}
/* Are we averaging over a dimension? */
average_data.averaging_over_dimension = (averaging_dimension != NULL);
/* Check for weights and width-weighting */
weights_specified = weights.numvalues > 0;
if (weights_specified && width_weighted) {
(void) fprintf(stderr,
"%s: Please do not specify weights and width-weighting.\n",
argv[0]);
exit(EXIT_FAILURE);
}
/* Default is no weighting */
average_data.num_weights = 0;
average_data.weights = NULL;
/* Check for weights */
if (weights_specified) {
if (averaging_dimension == NULL) {
if (weights.numvalues != nfiles) {
(void) fprintf(stderr,
"%s: Number of weights does not match number of files.\n",
argv[0]);
exit(EXIT_FAILURE);
}
}
else {
if (nfiles > 1) {
(void) fprintf(stderr,
"%s: Only one input file allowed with -weights and -avgdim.\n",
argv[0]);
exit(EXIT_FAILURE);
}
/* Check that the dimension size matches the number of weights */
first_mincid = miopen(infiles[0], NC_NOWRITE);
dimid = ncdimid(first_mincid, averaging_dimension);
(void) ncdiminq(first_mincid, dimid, NULL, &count);
if (weights.numvalues != count) {
(void) fprintf(stderr,
"%s: Number of weights does not match size of dimension.\n",
argv[0]);
}
}
/* Save the weights */
average_data.num_weights = weights.numvalues;
average_data.weights =
malloc(sizeof(*average_data.weights) * average_data.num_weights);
for (iweight=0; iweight < average_data.num_weights; iweight++) {
average_data.weights[iweight] = weights.values[iweight];
}
free(weights.values);
}
/* Check for width weighting */
if (width_weighted) {
/* Check for errors */
if (averaging_dimension == NULL) {
(void) fprintf(stderr,
"%s: Please specify -avgdim with -width_weighted.\n",
argv[0]);
exit(EXIT_FAILURE);
}
if (nfiles > 1) {
(void) fprintf(stderr,
"%s: Use -width_weighted with only one input file.\n",
argv[0]);
exit(EXIT_FAILURE);
}
/* Open the file */
first_mincid = miopen(infiles[0], NC_NOWRITE);
/* Get the dimension id */
dimid = ncdimid(first_mincid, averaging_dimension);
/* Look for the width variable */
strlength = MAX_NC_NAME - strlen(WIDTH_SUFFIX) - 1;
(void) strncpy(dimname, averaging_dimension, strlength);
dimname[strlength] = '\0';
(void) strcat(dimname, WIDTH_SUFFIX);
old_ncopts = ncopts; ncopts = 0;
varid = ncvarid(first_mincid, dimname);
(void) ncvarinq(first_mincid, varid, NULL, NULL, &ndims, dim, NULL);
ncopts = old_ncopts;
if (varid != MI_ERROR) {
/* Check that things match up */
if ((ndims != 1) || (dim[0] != dimid)) {
(void) fprintf(stderr,
"%s: Dimension width variable does not match avgdim.\n",
argv[0]);
}
/* Get the size of the dimension */
(void) ncdiminq(first_mincid, dim[0], NULL, &count);
average_data.num_weights = count;
average_data.weights =
malloc(sizeof(*average_data.weights) * average_data.num_weights);
/* Read in the widths */
start = 0;
(void) mivarget(first_mincid, varid, &start, &count, NC_DOUBLE, NULL,
average_data.weights);
}
} /* If width_weighted */
/* Check that weights sum to non-zero. We don't need to normalize them,
since a running sum is done in the averaging. */
if (average_data.num_weights > 0) {
total_weight = 0.0;
for (iweight=0; iweight < average_data.num_weights; iweight++) {
total_weight += average_data.weights[iweight];
}
if (total_weight == 0.0) {
(void) fprintf(stderr, "%s: Weights sum to zero.\n", argv[0]);
exit(EXIT_FAILURE);
}
}
/* If we don't have weights, each input will get a weight of 1 */
if (average_data.num_weights == 0)
total_weight = nfiles;
/* Check the cumulative weight thresholding */
if (weight_thresh > 0.0 && weight_thresh_fraction > 0.0){
(void) fprintf(stderr,
"Do not specify both -min_weight -min_weight_fraction\n");
exit(EXIT_FAILURE);
}
else if( weight_thresh_fraction > 0.0 ){
weight_thresh = weight_thresh_fraction * total_weight;
}
average_data.weight_thresh = weight_thresh;
/* Check for binarization */
if (binarize) {
if (normalize == TRUE) {
(void) fprintf(stderr,
"%s: Normalization and binarization cannot both be specified\n",
argv[0]);
exit(EXIT_FAILURE);
}
normalize = FALSE;
if (binvalue != -DBL_MAX) {
binrange[0] = binvalue - 0.5;
binrange[1] = binvalue + 0.5;
}
if (binrange[0] > binrange[1]) {
(void) fprintf(stderr,
"%s: Please specify a binarization range with min less than max\n",
argv[0]);
exit(EXIT_FAILURE);
}
average_data.binrange[0] = binrange[0];
average_data.binrange[1] = binrange[1];
}
average_data.binarize = binarize;
/* Store the ignore above/below values */
average_data.ignore_below = ignore_below;
average_data.ignore_above = ignore_above;
/* Check for no specification of normalization */
#ifdef NO_DEFAULT_NORM
if (normalize == -1) {
(void) fprintf(stderr, "\n%s: %s\n\n%s\n%s\n%s\n%s\n%s\n\n", argv[0],
"Please specify either -norm or -nonorm.",
"The default setting for normalization is being changed from \"-norm\" to",
"\"-nonorm\". To prevent undetected problems with data, this program will ",
"not work unless one of these flags is explicitly given on the command-line",
"(ie. no default is permitted). The new default will come into effect some",
"time in the future."
);
exit(EXIT_FAILURE);
}
#endif
/* Do normalization if needed */
average_data.norm_factor =
malloc(sizeof(*average_data.norm_factor) * nfiles);
if (normalize) {
vol_mean = malloc(sizeof(*vol_mean) * nfiles);
loop_options = create_loop_options();
set_loop_verbose(loop_options, FALSE);
#if MINC2
set_loop_v2format(loop_options, minc2_format);
#endif /* MINC2 */
set_loop_accumulate(loop_options, TRUE, 0, NULL, NULL);
set_loop_buffer_size(loop_options, (long) 1024 * max_buffer_size_in_kb);
set_loop_check_dim_info(loop_options, check_dimensions);
vol_total = 0.0;
nvols = 0;
if (verbose) {
(void) fprintf(stderr, "Normalizing:");
(void) fflush(stderr);
}
for (ifile=0; ifile < nfiles; ifile++) {
norm_data.threshold_set = FALSE;
norm_data.sum0 = 0.0;
norm_data.sum1 = 0.0;
if (verbose) {
(void) fprintf(stderr, ".");
(void) fflush(stderr);
}
if (first_mincid != MI_ERROR) {
set_loop_first_input_mincid(loop_options, first_mincid);
first_mincid = MI_ERROR;
}
voxel_loop(1, &infiles[ifile], 0, NULL, NULL, loop_options,
do_normalization, (void *) &norm_data);
if (norm_data.sum0 > 0.0) {
vol_mean[ifile] = norm_data.sum1 / norm_data.sum0;
vol_total += vol_mean[ifile];
nvols++;
}
else {
vol_mean[ifile] = 0.0;
}
if (debug) {
(void) fprintf(stderr, "Volume %d mean = %.15g\n",
ifile, vol_mean[ifile]);
}
}
free_loop_options(loop_options);
if (verbose) {
(void) fprintf(stderr, "Done\n");
(void) fflush(stderr);
}
if (nvols > 0)
global_mean = vol_total / nvols;
else
global_mean = 0.0;
for (ifile=0; ifile < nfiles; ifile++) {
if (vol_mean[ifile] > 0.0)
average_data.norm_factor[ifile] = global_mean / vol_mean[ifile];
else
average_data.norm_factor[ifile] = 0.0;
if (debug) {
(void) fprintf(stderr, "Volume %d norm factor = %.15g\n",
ifile, average_data.norm_factor[ifile]);
}
}
free(vol_mean);
}
else {
for (ifile=0; ifile < nfiles; ifile++) {
average_data.norm_factor[ifile] = 1.0;
}
}
/* Do averaging */
average_data.need_sd = (sdfile != NULL);
average_data.need_weight = (weightfile != NULL);
loop_options = create_loop_options();
if (first_mincid != MI_ERROR) {
set_loop_first_input_mincid(loop_options, first_mincid);
first_mincid = MI_ERROR;
}
set_loop_verbose(loop_options, verbose);
set_loop_clobber(loop_options, clobber);
set_loop_datatype(loop_options, datatype, is_signed,
valid_range[0], valid_range[1]);
set_loop_accumulate(loop_options, TRUE, 1, start_average, finish_average);
set_loop_copy_all_header(loop_options, copy_all_header);
set_loop_dimension(loop_options, averaging_dimension);
set_loop_buffer_size(loop_options, (long) 1024 * max_buffer_size_in_kb);
set_loop_check_dim_info(loop_options, check_dimensions);
voxel_loop(nfiles, infiles, nout, outfiles, arg_string, loop_options,
do_average, (void *) &average_data);
free_loop_options(loop_options);
/* Free stuff */
free(average_data.weights);
free(average_data.norm_factor);
exit(EXIT_SUCCESS);
}
int main(int argc, char *argv[]) {
int v1, v2, v3, v4;
int sizes[VIO_MAX_DIMENSIONS], grid_sizes[4];
int n_concat_transforms, i;
VIO_STR arg_string;
char *input_volume_name;
char *input_xfm;
VIO_STR outfile;
VIO_Real w1, w2, w3;
VIO_Real nw1, nw2, nw3;
VIO_Real original[3], transformed[3];
VIO_Real value;
VIO_Real cosine[3];
VIO_Real original_separation[3], grid_separation[4];
VIO_Real original_starts[3], grid_starts[4];
VIO_Volume eval_volume, new_grid;
VIO_General_transform xfm, *voxel_to_world;
VIO_STR *dimnames, dimnames_grid[4];
VIO_progress_struct progress;
arg_string = time_stamp(argc, argv);
/* Check arguments */
if(ParseArgv(&argc, argv, argTable, 0) || (argc != 4)){
fprintf(stderr, "\nUsage: %s [options] input.mnc input.xfm output_grid.mnc\n", argv[0]);
fprintf(stderr, " %s -help\n\n", argv[0]);
exit(EXIT_FAILURE);
}
input_volume_name = argv[1];
input_xfm = argv[2];
outfile = argv[3];
/* check for the infile and outfile */
if(access(input_volume_name, F_OK) != 0){
fprintf(stderr, "%s: Couldn't find %s\n\n", argv[0], input_volume_name);
exit(EXIT_FAILURE);
}
if(access(input_xfm, F_OK) != 0) {
fprintf(stderr, "%s: Couldn't find %s\n\n", argv[0], input_xfm);
exit(EXIT_FAILURE);
}
if(access(outfile, F_OK) == 0 && !clobber){
fprintf(stderr, "%s: %s exists! (use -clobber to overwrite)\n\n", argv[0], outfile);
exit(EXIT_FAILURE);
}
/*--- input the volume */
/*
if( input_volume( input_volume_name, 3, NULL, MI_ORIGINAL_TYPE,
FALSE, 0.0, 0.0, TRUE, &eval_volume,(minc_input_options *) NULL ) != OK )
return( 1 );
*/
if (input_volume_header_only( input_volume_name, 3, NULL, &eval_volume,(minc_input_options *) NULL ) != VIO_OK ) {
return( 1 );
}
/* get information about the volume */
get_volume_sizes( eval_volume, sizes );
voxel_to_world = get_voxel_to_world_transform(eval_volume);
dimnames = get_volume_dimension_names(eval_volume);
get_volume_separations(eval_volume, original_separation);
get_volume_starts(eval_volume, original_starts);
/* create new 4D volume, last three dims same as other volume,
first dimension being the vector dimension. */
for(i=1; i < 4; i++) {
dimnames_grid[i] = dimnames[i-1];
grid_separation[i] = original_separation[i-1];
grid_sizes[i] = sizes[i-1];
grid_starts[i] = original_starts[i-1];
}
dimnames_grid[0] = "vector_dimension";
grid_sizes[0] = 3;
grid_separation[0] = 1;
grid_starts[0] = 0;
new_grid = create_volume(4, dimnames_grid, NC_SHORT, FALSE, 0.0, 0.0);
//set_voxel_to_world_transform(new_grid, voxel_to_world);
// initialize the new grid volume, otherwise the output will be
// garbage...
set_volume_real_range(new_grid, -100, 100);
set_volume_sizes(new_grid, grid_sizes);
set_volume_separations(new_grid, grid_separation);
set_volume_starts(new_grid, grid_starts);
/*
for (i=0; i < 3; i++) {
get_volume_direction_cosine(eval_volume, i, cosine);
set_volume_direction_cosine(new_grid, i+1, cosine);
}
*/
alloc_volume_data(new_grid);
/* get the transforms */
if( input_transform_file( input_xfm, &xfm ) != VIO_OK )
return( 1 );
/* see how many transforms will be applied */
n_concat_transforms = get_n_concated_transforms( &xfm );
printf("Number of transforms to be applied: %d\n", n_concat_transforms);
initialize_progress_report(&progress, FALSE, sizes[0], "Processing");
/* evaluate the transform at every voxel, keep the displacement
in the three cardinal directions */
for( v1 = 0; v1 < sizes[0]; ++v1 ) {
update_progress_report(&progress, v1 + 1);
for( v2 = 0; v2 < sizes[1]; ++v2 ) {
for( v3 = 0; v3 < sizes[2]; ++v3 ) {
convert_3D_voxel_to_world(eval_volume,
v1, v2, v3,
&original[0], &original[1], &original[2]);
general_transform_point(&xfm,
original[0], original[1], original[2],
&transformed[0], &transformed[1], &transformed[2]);
for(i=0; i < 3; i++) {
value = transformed[i] - original[i];
set_volume_real_value(new_grid, i, v1, v2, v3, 0, value);
}
}
}
}
terminate_progress_report(&progress);
printf("Outputting volume.\n");
output_volume(outfile, MI_ORIGINAL_TYPE, TRUE, 0.0, 0.0, new_grid, arg_string, NULL);
return(0);
}
int
main(int argc, char **argv)
{
char *line_ptr;
int i;
char img_fname[1024];
char hdr_fname[1024];
char out_fname[1024];
int result;
if (ParseArgv(&argc, argv, argTable, 0) || argc < 2) {
usage(argv[0]);
return (-1);
}
ncopts = 0;
/* Set the dimension names. This is done here since the correct
* arrangement depends on the value of _orient_flag
*/
_dimnames[DIM_T] = MItime;
_dimnames[DIM_X] = MIxspace;
_dimnames[DIM_Y] = MIyspace;
_dimnames[DIM_Z] = MIzspace;
_dimnames[DIM_W] = MIvector_dimension;
if (_orient_flag == ORIENT_HEAD) {
/* If using head orientation, exchange Y and Z.
*/
_dimnames[DIM_Y] = MIzspace;
_dimnames[DIM_Z] = MIyspace;
}
/* Open the header and the associated binary file. */
for (i = 1; i < argc; i++) {
/* Here we try to be flexible about allowing the user to specify
* either the name of the .hdr file or the name of the .img file,
* or just the base name of the two files. All three options
* should work.
*/
strcpy(img_fname, argv[i]);
strcpy(hdr_fname, argv[i]);
/* Find the last extension.
*/
line_ptr = strrchr(argv[i], '.');
/* Did the user specify the .hdr file??
*/
if (line_ptr != NULL && !strcmp(line_ptr, ".hdr")) {
line_ptr = strrchr(img_fname, '.');
if (line_ptr != NULL) {
*line_ptr = '\0';
}
}
/* Did the user specify the .img file??
*/
else if (line_ptr != NULL && !strcmp(line_ptr, ".img")) {
strcat(hdr_fname, ".hdr");
}
/* Or perhaps just the base name??
*/
else {
strcat(img_fname, ".img");
strcat(hdr_fname, ".img.hdr");
}
/* See if there is a filename following this one, and if so, does it
* end with the ".mnc" extension. If so, take that names as the
* output for this conversions.
*/
if (i < argc - 1 &&
(line_ptr = strrchr(argv[i+1], '.')) != NULL &&
!strcmp(line_ptr, ".mnc")) {
strcpy(out_fname, argv[i+1]);
i++;
}
else {
strcpy(out_fname, img_fname);
line_ptr = strrchr(out_fname, '.');
if (line_ptr != NULL) {
strcpy(line_ptr, ".mnc");
}
}
/* Perform the conversion.
*/
message(MSG_INFO, "Starting conversion\n");
message(MSG_INFO, "- Input header: %s\n", hdr_fname);
message(MSG_INFO, "- Input image: %s\n", img_fname);
message(MSG_INFO, "- Output file: %s\n", out_fname);
result = upet_to_minc(hdr_fname, img_fname, out_fname, argv[0]);
if (result < 0) {
message(MSG_ERROR, "Error creating %s\n", out_fname);
}
else {
message(MSG_INFO, "Finished creating %s\n", out_fname);
}
}
return 0;
}
