/* regrid using a minc volume */
void regrid_minc(char *in_fn, int buffer_size,
VIO_Volume * totals, VIO_Volume * weights, int v_size,
double regrid_floor, double regrid_ceil)
{
Loop_Data ld;
Loop_Options *loop_opt;
int mincid;
/* Open the file to get some information */
mincid = miopen(in_fn, NC_NOWRITE);
ld.file_ndims = get_minc_ndims(mincid);
get_minc_spatial_dims(mincid, ld.space_to_dim, ld.dim_to_space);
get_minc_voxel_to_world(mincid, ld.voxel_to_world);
/* alloc space for data_buf */
ld.data_buf = (double *)malloc(sizeof(double) * v_size);
ld.floor = regrid_floor;
ld.ceil = regrid_ceil;
ld.totals = totals;
ld.weights = weights;
/* set up and do voxel_loop */
loop_opt = create_loop_options();
set_loop_first_input_mincid(loop_opt, mincid);
set_loop_verbose(loop_opt, verbose);
set_loop_buffer_size(loop_opt, (long)1024 * buffer_size);
voxel_loop(1, &in_fn, 0, NULL, NULL, loop_opt, regrid_loop, (void *)&ld);
free_loop_options(loop_opt);
/* tidy up */
free(ld.data_buf);
}
/* get info from a model file (steps, starts, etc */
int get_model_file_info(char *dst, char *key, char *nextArg)
{
int mincid;
char *fname;
/* Get pointer to volume definition structure */
Volume_Definition *vd = (Volume_Definition *) dst;
/* Check for following argument */
if(nextArg == NULL){
(void)fprintf(stderr, "\"%s\" option requires an additional argument\n", key);
exit(EXIT_FAILURE);
}
fname = nextArg;
/* check that the file exists */
if(!file_exists(fname)){
fprintf(stderr, "Couldn't find -like file %s.\n\n", fname);
exit(EXIT_FAILURE);
}
/* get volume definition from input filename */
mincid = miopen(fname, NC_NOWRITE);
get_vol_def(mincid, vd);
/* Close the file */
miclose(mincid);
return TRUE;
}
MNCAPI int minc_format_convert(const char *input,const char *output)
{
int old_fd;
int new_fd;
int flags;
struct mi2opts opts;
old_fd = miopen((char *)input, NC_NOWRITE);
if (old_fd < 0) {
perror(input);
return MI_ERROR;
}
flags = NC_CLOBBER|MI2_CREATE_V2;
memset(&opts,0,sizeof(struct mi2opts));
opts.struct_version = MI2_OPTS_V1;
new_fd = micreatex((char *)output, flags, &opts);
if (new_fd < 0) {
perror(output);
exit MI_ERROR;
}
micopy(old_fd, new_fd);
miclose(old_fd);
miclose(new_fd);
return MI_NOERROR;
}
MNCAPI int
minc_get_world_transform(char *path, double transform[MINC_3D][MINC_3D+1])
{
int i, j;
double dircos[MINC_3D];
double step, start;
char *dimensions[] = { MIxspace, MIyspace, MIzspace };
int length;
int fd;
int varid;
int old_ncopts;
old_ncopts =get_ncopts();
set_ncopts(0);
fd = miopen(path, NC_NOWRITE);
if (fd < 0) {
set_ncopts(old_ncopts);
return (MINC_STATUS_ERROR);
}
/* Zero the matrix */
for (i = 0; i < MINC_3D; i++) {
for (j = 0; j < MINC_3D + 1; j++) {
transform[i][j] = 0.0;
}
transform[i][i] = 1.0;
}
for (j = 0; j < MINC_3D; j++) {
/* Set default values */
step = 1.0;
start = 0.0;
for (i = 0; i < MINC_3D; i++) {
dircos[i] = 0.0;
}
dircos[j] = 1.0;
varid = ncvarid(fd, dimensions[j]);
miattget(fd, varid, MIstart, NC_DOUBLE, 1, &start, &length);
miattget(fd, varid, MIstep, NC_DOUBLE, 1, &step, &length);
miattget(fd, varid, MIdirection_cosines, NC_DOUBLE, 3, dircos, &length);
normalize_vector(dircos);
/* Put them in the matrix.
*/
for (i = 0; i < MINC_3D; i++) {
transform[i][j] = step * dircos[i];
transform[i][MINC_3D] += start * dircos[i];
}
}
set_ncopts(old_ncopts);
return (MINC_STATUS_OK);
}
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);
}
/* ----------------------------- MNI Header -----------------------------------
@NAME : get_volume_info
@INPUT : infile - input file name
@OUTPUT : volume_info - input volume information
@RETURNS : Id of icv created
@DESCRIPTION: Routine to read volume information for a file.
@METHOD :
@GLOBALS :
@CALLS :
@CREATED : August 22, 1993 (Peter Neelin)
@MODIFIED :
---------------------------------------------------------------------------- */
static int get_volume_info(char *infile, Volume_Info *volume_info)
{
int icvid, mincid;
/* Create and set up icv for input */
icvid = miicv_create();
setup_input_icv(icvid);
/* Open the image file */
mincid = miopen(infile, NC_NOWRITE);
/* Attach the icv to the file */
(void) miicv_attach(icvid, mincid, ncvarid(mincid, MIimage));
/* Get dimension information */
get_dimension_info(infile, icvid, volume_info);
/* Get the volume min and max */
(void) miicv_inqdbl(icvid, MI_ICV_NORM_MIN, &volume_info->minimum);
(void) miicv_inqdbl(icvid, MI_ICV_NORM_MAX, &volume_info->maximum);
return icvid;
}
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
test_icv_read(char *filename, int xsize, int ysize, double image_min,
double image_max, nc_type datatype, char *signtype)
{
int icv, cdfid, img, ndims;
static long coord[MAX_VAR_DIMS];
static long count[MAX_VAR_DIMS];
int dim[MAX_VAR_DIMS];
long dim_size;
unsigned char *image;
int i;
double min, max;
int n;
min = DBL_MAX;
max = -DBL_MAX;
image = malloc(xsize * ysize * nctypelen(datatype));
if (image == NULL) {
return (ERROR_STATUS);
}
/* Create the icv */
icv=miicv_create();
(void) miicv_setint(icv, MI_ICV_XDIM_DIR, MI_ICV_POSITIVE);
(void) miicv_setint(icv, MI_ICV_YDIM_DIR, MI_ICV_POSITIVE);
(void) miicv_setint(icv, MI_ICV_ZDIM_DIR, MI_ICV_POSITIVE);
(void) miicv_setint(icv, MI_ICV_ADIM_SIZE, xsize);
(void) miicv_setint(icv, MI_ICV_BDIM_SIZE, ysize);
(void) miicv_setint(icv, MI_ICV_KEEP_ASPECT, FALSE);
(void) miicv_setint(icv, MI_ICV_DO_DIM_CONV, TRUE);
(void) miicv_setint(icv, MI_ICV_TYPE, datatype);
(void) miicv_setstr(icv, MI_ICV_SIGN, signtype);
(void) miicv_setdbl(icv, MI_ICV_VALID_MAX, image_max);
(void) miicv_setdbl(icv, MI_ICV_VALID_MIN, image_min);
/* Open the file, attach the image variable */
cdfid=miopen(filename, NC_NOWRITE);
/* Attach image variable */
img=ncvarid(cdfid, MIimage);
(void) miicv_attach(icv, cdfid, img);
/* Get the number of dimensions and modify count and coord */
(void) ncvarinq(cdfid, img, NULL, NULL, &ndims, dim, NULL);
if (ndims!=3) {
(void) fprintf(stderr, "File must have 3 dimensions\n");
return ERROR_STATUS;
}
(void) ncdiminq(cdfid, dim[0], NULL, &dim_size);
count[0]=1;
count[1]=ysize;
count[2]=xsize;
coord[1]=0;
coord[2]=0;
/* Get the data */
for (i=0; i<dim_size; i++) {
coord[0]=i;
(void) miicv_get(icv, coord, count, image);
switch (datatype) {
case NC_BYTE:
if (!strcmp(signtype, MI_UNSIGNED)) {
for (n = 0; n < xsize*ysize; n++) {
unsigned char uc = *(((unsigned char *)image) + n);
if (uc > max) {
max = uc;
}
if (uc < min) {
min = uc;
}
}
}
else {
for (n = 0; n < xsize*ysize; n++) {
signed char sc = *(((signed char *)image) + n);
if (sc > max) {
max = sc;
}
if (sc < min) {
min = sc;
}
}
}
break;
case NC_SHORT:
if (!strcmp(signtype, MI_UNSIGNED)) {
for (n = 0; n < xsize*ysize; n++) {
unsigned short uc = *(((unsigned short *)image) + n);
if (uc > max) {
max = uc;
}
if (uc < min) {
min = uc;
}
}
}
else {
for (n = 0; n < xsize*ysize; n++) {
signed short sc = *(((signed short *)image) + n);
if (sc > max) {
max = sc;
}
if (sc < min) {
min = sc;
}
}
}
break;
case NC_INT:
if (!strcmp(signtype, MI_UNSIGNED)) {
for (n = 0; n < xsize*ysize; n++) {
unsigned int uc = *(((unsigned int *)image) + n);
if (uc > max) {
max = uc;
}
if (uc < min) {
min = uc;
}
}
}
else {
for (n = 0; n < xsize*ysize; n++) {
signed int sc = *(((signed int *)image) + n);
if (sc > max) {
max = sc;
}
if (sc < min) {
min = sc;
}
}
}
break;
case NC_FLOAT:
for (n = 0; n < xsize*ysize; n++) {
float sc = *(((float *)image) + n);
if (sc > max) {
max = sc;
}
if (sc < min) {
min = sc;
}
}
break;
case NC_DOUBLE:
for (n = 0; n < xsize*ysize; n++) {
double sc = *(((double *)image) + n);
if (sc > max) {
max = sc;
}
if (sc < min) {
min = sc;
}
}
break;
}
printf("%d %s %s %f %f\n", i, signtype, nctypename(datatype), min, max);
}
/* Close the file and free the icv */
(void) miclose(cdfid);
(void) miicv_free(icv);
free(image);
return (NORMAL_STATUS);
}
MNCAPI int
minc_load_data(char *path, void *dataptr, int datatype,
long *ct, long *cz, long *cy, long *cx,
double *dt, double *dz, double *dy, double *dx,
void **infoptr)
{
int fd; /* MINC file descriptor */
nc_type nctype; /* netCDF type */
char *signstr; /* MI_SIGNED or MI_UNSIGNED */
int length;
int dim_id[MI_S_NDIMS];
long dim_len[MI_S_NDIMS];
int i, j; /* Generic loop counters */
int var_id;
int var_ndims;
int var_dims[MAX_NC_DIMS];
int icv; /* MINC image conversion variable */
long start[MI_S_NDIMS];
long count[MI_S_NDIMS];
size_t ucount[MI_S_NDIMS];
int dir[MI_S_NDIMS]; /* Dimension "directions" */
int map[MI_S_NDIMS]; /* Dimension mapping */
int old_ncopts; /* For storing the old state of ncopts */
double *p_dtmp;
long *p_ltmp;
struct file_info *p_file;
struct att_info *p_att;
int r; /* Generic return code */
*infoptr = NULL;
fd = miopen(path, NC_NOWRITE);
if (fd < 0) {
return (MINC_STATUS_ERROR);
}
old_ncopts =get_ncopts();
set_ncopts(0);
for (i = 0; i < MI_S_NDIMS; i++) {
dim_id[i] = ncdimid(fd, minc_dimnames[i]);
if (dim_id[i] >= 0) {
ncdiminq(fd, dim_id[i], NULL, &dim_len[i]);
var_id = ncvarid(fd, minc_dimnames[i]);
ncattinq(fd, var_id, MIstep, &nctype, &length);
switch (i) {
case MI_S_T:
p_ltmp = ct;
p_dtmp = dt;
break;
case MI_S_X:
p_ltmp = cx;
p_dtmp = dx;
break;
case MI_S_Y:
p_ltmp = cy;
p_dtmp = dy;
break;
case MI_S_Z:
p_ltmp = cz;
p_dtmp = dz;
break;
default:
return (MINC_STATUS_ERROR);
}
if (nctype == NC_DOUBLE && length == 1) {
ncattget(fd, var_id, MIstep, p_dtmp);
}
else {
*p_dtmp = 0; /* Unknown/not set */
}
*p_ltmp = dim_len[i];
}
else {
dim_len[i] = 0;
}
}
set_ncopts(old_ncopts);
var_id = ncvarid(fd, MIimage);
ncvarinq(fd, var_id, NULL, &nctype, &var_ndims, var_dims, NULL);
if (var_ndims != 3 && var_ndims != 4) {
return (MINC_STATUS_ERROR);
}
/* We want the data to wind up in t, x, y, z order. */
for (i = 0; i < MI_S_NDIMS; i++) {
map[i] = -1;
}
for (i = 0; i < var_ndims; i++) {
if (var_dims[i] == dim_id[MI_S_T]) {
map[MI_S_T] = i;
}
else if (var_dims[i] == dim_id[MI_S_X]) {
map[MI_S_X] = i;
}
else if (var_dims[i] == dim_id[MI_S_Y]) {
map[MI_S_Y] = i;
}
else if (var_dims[i] == dim_id[MI_S_Z]) {
map[MI_S_Z] = i;
}
}
icv = miicv_create();
minc_simple_to_nc_type(datatype, &nctype, &signstr);
miicv_setint(icv, MI_ICV_TYPE, nctype);
miicv_setstr(icv, MI_ICV_SIGN, signstr);
miicv_attach(icv, fd, var_id);
for (i = 0; i < var_ndims; i++) {
start[i] = 0;
}
for (i = 0; i < MI_S_NDIMS; i++) {
if (map[i] >= 0) {
count[map[i]] = dim_len[i];
}
}
r = miicv_get(icv, start, count, dataptr);
if (r < 0) {
return (MINC_STATUS_ERROR);
}
if (map[MI_S_T] >= 0) {
if (*dt < 0) {
dir[MI_S_T] = -1;
*dt = -*dt;
}
else {
dir[MI_S_T] = 1;
}
}
if (map[MI_S_X] >= 0) {
if (*dx < 0) {
dir[MI_S_X] = -1;
*dx = -*dx;
}
else {
dir[MI_S_X] = 1;
}
}
if (map[MI_S_Y] >= 0) {
if (*dy < 0) {
dir[MI_S_Y] = -1;
*dy = -*dy;
}
else {
dir[MI_S_Y] = 1;
}
}
if (map[MI_S_Z] >= 0) {
if (*dz < 0) {
dir[MI_S_Z] = -1;
*dz = -*dz;
}
else {
dir[MI_S_Z] = 1;
}
}
if (var_ndims == 3) {
for (i = 1; i < MI_S_NDIMS; i++) {
map[i-1] = map[i];
dir[i-1] = dir[i];
}
}
j = 0;
for (i = 0; i < MI_S_NDIMS; i++) {
if (dim_len[i] > 0) {
ucount[j++] = dim_len[i];
}
}
restructure_array(var_ndims, dataptr, ucount, nctypelen(nctype),
map, dir);
miicv_detach(icv);
miicv_free(icv);
old_ncopts =get_ncopts();
set_ncopts(0);
/* Generate the complete infoptr array.
* This is essentially an in-memory copy of the variables and attributes
* in the file.
*/
p_file = (struct file_info *) malloc(sizeof (struct file_info));
ncinquire(fd, &p_file->file_ndims, &p_file->file_nvars,
&p_file->file_natts, NULL);
p_file->file_atts = (struct att_info *) malloc(sizeof (struct att_info) *
p_file->file_natts);
p_file->file_vars = (struct var_info *) malloc(sizeof (struct var_info) *
p_file->file_nvars);
for (i = 0; i < p_file->file_natts; i++) {
p_att = &p_file->file_atts[i];
ncattname(fd, NC_GLOBAL, i, p_att->att_name);
ncattinq(fd, NC_GLOBAL,
p_att->att_name,
&p_att->att_type,
&p_att->att_len);
p_att->att_val = malloc(p_att->att_len * nctypelen(p_att->att_type));
ncattget(fd, NC_GLOBAL, p_att->att_name, p_att->att_val);
}
for (i = 0; i < p_file->file_nvars; i++) {
struct var_info *p_var = &p_file->file_vars[i];
ncvarinq(fd, i,
p_var->var_name,
&p_var->var_type,
&p_var->var_ndims,
p_var->var_dims,
&p_var->var_natts);
p_var->var_atts = malloc(p_var->var_natts *
sizeof (struct att_info));
if (ncdimid(fd, p_var->var_name) >= 0) {
/* It's a dimension variable, have to treat it specially... */
}
for (j = 0; j < p_var->var_natts; j++) {
p_att = &p_var->var_atts[j];
ncattname(fd, i, j, p_att->att_name);
ncattinq(fd, i,
p_att->att_name,
&p_att->att_type,
&p_att->att_len);
p_att->att_val = malloc(p_att->att_len * nctypelen(p_att->att_type));
ncattget(fd, i, p_att->att_name, p_att->att_val);
}
}
*infoptr = p_file;
set_ncopts(old_ncopts);
miclose(fd);
return (MINC_STATUS_OK);
}
MNCAPI int
minc_file_size(char *path,
long *ct, long *cz, long *cy, long *cx,
long *cvoxels, long *cbytes)
{
int fd;
nc_type nctype;
int dim_id[MI_S_NDIMS];
long dim_len[MI_S_NDIMS];
int i;
int var_id;
int var_ndims;
int var_dims[MAX_NC_DIMS];
long voxel_count;
long byte_count;
int old_ncopts;
fd = miopen(path, NC_NOWRITE);
if (fd < 0) {
return (MINC_STATUS_ERROR);
}
old_ncopts =get_ncopts();
set_ncopts(0);
for (i = 0; i < MI_S_NDIMS; i++) {
dim_id[i] = ncdimid(fd, minc_dimnames[i]);
if (dim_id[i] >= 0) {
ncdiminq(fd, dim_id[i], NULL, &dim_len[i]);
}
else {
dim_len[i] = 0;
}
}
set_ncopts(old_ncopts);
if (ct != NULL) {
*ct = dim_len[MI_S_T];
}
if (cz != NULL) {
*cz = dim_len[MI_S_Z];
}
if (cy != NULL) {
*cy = dim_len[MI_S_Y];
}
if (cx != NULL) {
*cx = dim_len[MI_S_X];
}
var_id = ncvarid(fd, MIimage);
if (cvoxels != NULL || cbytes != NULL) {
ncvarinq(fd, var_id, NULL, &nctype, &var_ndims, var_dims, NULL);
voxel_count = 1;
for (i = 0; i < var_ndims; i++) {
long length;
ncdiminq(fd, var_dims[i], NULL, &length);
voxel_count *= length;
}
byte_count = voxel_count * nctypelen(nctype);
if (cvoxels != NULL) {
*cvoxels = voxel_count;
}
if (cbytes != NULL) {
*cbytes = byte_count;
}
}
return (MINC_STATUS_OK);
}
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[])
{
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[])
{
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[])
{
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);
}