int main()
{
int cdf, cdf2;
int img;
int dim[MAX_VAR_DIMS];
int dim2[MAX_VAR_DIMS];
long start[MAX_VAR_DIMS];
long count[MAX_VAR_DIMS];
double image[256*256];
int i, j, k, ioff;
char filename[256];
char filename2[256];
set_ncopts(NC_VERBOSE|NC_FATAL);
snprintf(filename, sizeof(filename), "test_minc-%d.mnc", getpid());
snprintf(filename2, sizeof(filename2), "test_minc2-%d.mnc", getpid());
cdf=micreate(filename, NC_CLOBBER);
count[2]=5;
count[1]=3;
count[0]=7;
dim[2]=ncdimdef(cdf, MIzspace, count[2]);
dim[1]=ncdimdef(cdf, MIxspace, count[1]);
dim[0]=ncdimdef(cdf, MIyspace, count[0]);
dim2[0]=ncdimdef(cdf, MItime, NC_UNLIMITED);
dim2[1]=dim[0];
dim2[2]=dim[1];
img=ncvardef(cdf, MIimage, NC_SHORT, 3, dim);
(void) ncvardef(cdf, "testvar", NC_FLOAT, 2, dim2);
(void) miattputstr(cdf, img, MIsigntype, MI_SIGNED);
for (j=0; j<count[0]; j++) {
for (i=0; i<count[1]; i++) {
ioff=(j*count[1]+i)*count[2];
for (k=0; k<count[2]; k++)
image[ioff+k]=ioff+k+10;
}
}
cdf2=micreate(filename2,NC_CLOBBER);
(void) ncdimdef(cdf2, "junkdim", NC_UNLIMITED);
(void) micopy_all_var_defs(cdf, cdf2, 1, &img);
(void) ncendef(cdf2);
(void) ncendef(cdf);
(void) miset_coords(3,0L,start);
(void) mivarput(cdf, img, start, count, NC_DOUBLE, NULL, image);
(void) micopy_all_var_values(cdf, cdf2, 1, &img);
(void) miclose(cdf2);
(void) miclose(cdf);
unlink(filename);
unlink(filename2);
return(0);
}
/* ----------------------------- MNI Header -----------------------------------
@NAME : save_volume_info
@INPUT : input_icvid - input file icvid (MI_ERROR means no input volume)
outfile - output file name
arg_string - string giving argument list
volume_info - volume information
@OUTPUT : (nothing)
@RETURNS : icv of output file
@DESCRIPTION: Routine to save a 3-D volume, copying information
from an optional input file.
@METHOD :
@GLOBALS :
@CALLS :
@CREATED : August 22, 1993 (Peter Neelin)
@MODIFIED :
---------------------------------------------------------------------------- */
static int save_volume_info(int input_icvid, char *outfile, char *arg_string,
Volume_Info *volume_info)
{
int mincid, icvid, inmincid;
/* Create output file */
mincid = micreate(outfile, NC_NOCLOBBER);
/* Open the input file if it is provided */
inmincid = MI_ERROR;
if (input_icvid != MI_ERROR) {
(void) miicv_inqint(input_icvid, MI_ICV_CDFID, &inmincid);
}
/* Set up variables and put output file in data mode */
setup_variables(inmincid, mincid, volume_info, arg_string);
/* Create an icv and set it up */
icvid = miicv_create();
setup_output_icv(icvid);
/* Attach the icv to the file */
(void) miicv_attach(icvid, mincid, ncvarid(mincid, MIimage));
return icvid;
}
int main(int argc, char **argv)
{
int cdf;
int img, img2;
int dim[MAX_VAR_DIMS];
long start[MAX_VAR_DIMS];
long count[MAX_VAR_DIMS];
double image[256*256];
int i, itype, jtype;
int cflag = 0;
char filename[256];
#if MINC2
if (argc == 2 && !strcmp(argv[1], "-2")) {
cflag = MI2_CREATE_V2;
}
#endif /* MINC2 */
snprintf(filename, sizeof(filename), "test_minc_types-%d.mnc", getpid());
ncopts=NC_VERBOSE|NC_FATAL;
for (itype=0; itype<ntypes; itype++) {
for (jtype=0; jtype<ntypes; jtype++) {
cdf=micreate(filename, NC_CLOBBER | cflag);
count[2]=256;
count[1]=20;
count[0]=7;
dim[2]=ncdimdef(cdf, MIzspace, count[2]);
dim[1]=ncdimdef(cdf, MIxspace, count[1]);
dim[0]=ncdimdef(cdf, MIyspace, count[0]);
img=ncvardef(cdf, MIimage, types[itype].type, 1, dim);
(void) miattputstr(cdf, img, MIsigntype, types[itype].sign);
img2=ncvardef(cdf, "image2", types[jtype].type, 1, dim);
(void) miattputstr(cdf, img2, MIsigntype, types[jtype].sign);
image[0]=10.0;
image[1]=2.0*(-FLT_MAX);
image[2]=2.0*FLT_MAX;
image[3]=3.2;
image[4]=3.7;
image[5]=(-3.2);
image[6]=(-3.7);
#if 0
for (j=0; j<count[0]; j++) {
for (i=0; i<count[1]; i++) {
ioff=(j*count[1]+i)*count[2];
for (k=0; k<count[2]; k++)
image[ioff+k]=ioff+k+10;
}
}
#endif
(void) ncendef(cdf);
(void) miset_coords(3,0L,start);
(void) mivarput(cdf, img, start, count, NC_DOUBLE, NULL, image);
(void) mivarget(cdf, img, start, count, types[jtype].type,
types[jtype].sign, image);
(void) mivarput(cdf, img2, start, count, types[jtype].type,
types[jtype].sign, image);
(void) mivarget(cdf, img2, start, count, NC_DOUBLE, NULL, image);
(void) printf("Image 1 : %s %s\n",types[itype].sign,
types[itype].ctype);
(void) printf("Image 2 : %s %s\n",types[jtype].sign,
types[jtype].ctype);
for (i=0;i<count[0];i++)
(void) printf(" image[%d] = %g\n",(int) i, image[i]);
(void) miclose(cdf);
}
}
unlink(filename);
return(0);
}
int main(int argc, char **argv)
{
int icv, cdfid, img, max, min, dimvar;
static int dim[MAX_VAR_DIMS];
static struct { long len; char *name;} diminfo[] = {
{ 7, MIzspace },
{ 9, MIyspace },
{ 2, MIxspace }
};
/* static struct { long len; char *name;} diminfo[]=
{3, MIzspace, 4, MIyspace, 5, MIxspace}; */
static int numdims=sizeof(diminfo)/sizeof(diminfo[0]);
static long coord[]={0,0,0};
static long count[]={3,4,5};
double dvalue;
short int ivalue[]={
111, 113, 115, 117, 119,
121, 123, 125, 127, 129,
131, 133, 135, 137, 139,
141, 143, 145, 147, 149,
211, 213, 215, 217, 219,
221, 223, 225, 227, 229,
231, 233, 235, 237, 239,
241, 243, 245, 247, 249,
311, 313, 315, 317, 319,
321, 323, 325, 327, 329,
331, 333, 335, 337, 339,
341, 343, 345, 347, 349
};
int i, j, k;
int cflag = 0;
#if MINC2
if (argc == 2 && !strcmp(argv[1], "-2")) {
cflag = MI2_CREATE_V2;
}
#endif /* MINC2 */
icv=miicv_create();
miicv_setint(icv, MI_ICV_XDIM_DIR, MI_ICV_NEGATIVE);
miicv_setint(icv, MI_ICV_YDIM_DIR, MI_ICV_NEGATIVE);
miicv_setint(icv, MI_ICV_ZDIM_DIR, MI_ICV_NEGATIVE);
miicv_setint(icv, MI_ICV_NUM_IMGDIMS, 3);
miicv_setint(icv, MI_ICV_DIM_SIZE+0, 5);
miicv_setint(icv, MI_ICV_DIM_SIZE+1, 4);
miicv_setint(icv, MI_ICV_DIM_SIZE+2, 3);
miicv_setint(icv, MI_ICV_DO_DIM_CONV, TRUE);
miicv_setint(icv, MI_ICV_KEEP_ASPECT, FALSE);
miicv_setint(icv, MI_ICV_DO_NORM, TRUE);
cdfid=micreate("test.mnc", NC_CLOBBER | cflag);
for (i=0; i<numdims; i++) {
dim[i]=ncdimdef(cdfid, diminfo[i].name, diminfo[i].len);
dimvar=micreate_std_variable(cdfid, diminfo[i].name, NC_DOUBLE,
0, &dim[i]);
miattputdbl(cdfid, dimvar, MIstep, 0.8);
miattputdbl(cdfid, dimvar, MIstart, 22.0);
}
img=micreate_std_variable(cdfid, MIimage, NC_SHORT,
numdims, dim);
max=micreate_std_variable(cdfid, MIimagemax, NC_DOUBLE, 1, dim);
min=micreate_std_variable(cdfid, MIimagemin, NC_DOUBLE, 1, dim);
ncendef(cdfid);
for (i=0; i<diminfo[0].len; i++) {
dvalue = 200;
coord[0]=i;
ncvarput1(cdfid, max, coord, &dvalue);
dvalue = -dvalue;
ncvarput1(cdfid, min, coord, &dvalue);
}
coord[0]=0;
miicv_attach(icv, cdfid, img);
miicv_inqdbl(icv, MI_ICV_ADIM_START, &dvalue);
printf("adim start = %g", dvalue);
miicv_inqdbl(icv, MI_ICV_ADIM_STEP, &dvalue);
printf(", step = %g\n", dvalue);
miicv_inqdbl(icv, MI_ICV_BDIM_START, &dvalue);
printf("bdim start = %g", dvalue);
miicv_inqdbl(icv, MI_ICV_BDIM_STEP, &dvalue);
printf(", step = %g\n", dvalue);
miicv_inqdbl(icv, MI_ICV_NORM_MAX, &dvalue);
printf("norm : max = %g", dvalue);
miicv_inqdbl(icv, MI_ICV_NORM_MIN, &dvalue);
printf(", min = %g\n", dvalue);
miicv_put(icv, coord, count, ivalue);
miicv_get(icv, coord, count, ivalue);
for (i=0; i<3; i++) {
for (j=0; j<4; j++) {
for (k=0; k<5; k++) {
printf("%5d",ivalue[i*20+j*5+k]);
}
printf("\n");
}
}
miclose(cdfid);
miicv_free(icv);
return 0;
}
int main(int argc, char **argv)
{
int icv, cdfid, img, max, min;
static char *typenm[]={"short", "double"};
static char *boolnm[] = {"true", "false"};
static nc_type intypes[] = {NC_SHORT, NC_DOUBLE};
static int norms[] = {TRUE, FALSE};
static nc_type outtypes[] = {NC_SHORT, NC_DOUBLE};
static int maxpresent[] = {TRUE, FALSE};
static int valpresent[] = {TRUE, FALSE};
static int dim[MAX_VAR_DIMS];
static struct { long len; char *name;} diminfo[] = {
{ 3, MIzspace },
{ 1, MIyspace },
{ 1, MIxspace }
};
static int numdims=sizeof(diminfo)/sizeof(diminfo[0]);
static long coord[]={0,0,0};
static long count[]={1,1,1};
static double max_values[] = {0.4, 0.6, 0.8};
double dvalue;
short int ivalue;
int i, intype, inorm, outtype, imax, ival;
int cflag = 0;
char filename[256];
#if MINC2
if (argc == 2 && !strcmp(argv[1], "-2")) {
cflag = MI2_CREATE_V2;
}
#endif /* MINC2 */
snprintf(filename, sizeof(filename), "test_icv_range-%d.mnc", getpid());
for (intype=0; intype<MAX_IN_TYPES; intype++) {
for (inorm=0; inorm<MAX_NORM; inorm++) {
icv=miicv_create();
miicv_setint(icv, MI_ICV_TYPE, intypes[intype]);
miicv_setint(icv, MI_ICV_DO_NORM, norms[inorm]);
miicv_setdbl(icv, MI_ICV_VALID_MAX, 20000.0);
miicv_setdbl(icv, MI_ICV_VALID_MIN, 0.0);
for (outtype=0; outtype<MAX_OUT_TYPES; outtype++) {
for (imax=0; imax<MAX_MAX; imax++) {
for (ival=0; ival<MAX_VAL; ival++) {
printf(
"in : %s, out : %s, norm : %s, imgmax : %s, valid : %s\n",
typenm[intype], typenm[outtype], boolnm[inorm],
boolnm[imax], boolnm[ival]);
cdfid=micreate(filename, NC_CLOBBER | cflag);
for (i=0; i<numdims; i++)
dim[i]=ncdimdef(cdfid, diminfo[i].name, diminfo[i].len);
img=micreate_std_variable(cdfid, MIimage, outtypes[outtype],
numdims, dim);
if (maxpresent[imax]) {
max=micreate_std_variable(cdfid, MIimagemax, NC_DOUBLE,
1, dim);
min=micreate_std_variable(cdfid, MIimagemin, NC_DOUBLE,
1, dim);
}
if (valpresent[ival]) {
dvalue = 32000;
ncattput(cdfid, img, MIvalid_max, NC_DOUBLE, 1, &dvalue);
dvalue = 0;
ncattput(cdfid, img, MIvalid_min, NC_DOUBLE, 1, &dvalue);
}
ncendef(cdfid);
if (maxpresent[imax]) {
for (i=0; i<3; i++) {
dvalue = max_values[i];
coord[0]=i;
ncvarput1(cdfid, max, coord, &dvalue);
dvalue = -dvalue;
ncvarput1(cdfid, min, coord, &dvalue);
}
coord[0]=0;
}
miicv_attach(icv, cdfid, img);
if (intypes[intype]==NC_DOUBLE) {
dvalue = 0.2;
miicv_put(icv, coord, count, &dvalue);
}
else {
ivalue = 12500;
miicv_put(icv, coord, count, &ivalue);
}
dvalue = 0;
mivarget1(cdfid, img, coord, NC_DOUBLE, MI_SIGNED, &dvalue);
printf(" file value = %g\n", dvalue);
if (intypes[intype]==NC_DOUBLE) {
miicv_get(icv, coord, count, &dvalue);
}
else {
miicv_get(icv, coord, count, &ivalue);
dvalue=ivalue;
}
printf(" icv value = %g\n", dvalue);
miclose(cdfid);
}
}
}
miicv_free(icv);
}
}
unlink(filename);
return 0;
}
MNCAPI int
minc_save_start(char *path, /* Path to the file */
int filetype, /* Date type as stored in the file */
long ct, /* Total length of time axis, in voxels */
long cz, /* Total length of Z axis, in voxels */
long cy, /* Total length of Y axis, in voxels */
long cx, /* Total length of X axis, in voxels */
double dt, /* Sample width along time axis, in seconds */
double dz, /* Sample width along Z axis, in mm */
double dy, /* Sample width along Y axis, in mm */
double dx, /* Sample width along X axis, in mm */
void *infoptr, /* Opaque file structure information */
const char *history) /* New history information */
{
int fd; /* MINC file descriptor */
int dim_id[MI_S_NDIMS]; /* netCDF dimension ID array */
int var_ndims; /* Number of dimensions per variable */
int var_dims[MI_S_NDIMS]; /* Dimension ID's per variable */
int i, j; /* Generic loop counters */
int old_ncopts; /* For supressing fatal error messages */
struct file_info *p_file; /* For accessing the file structure */
struct var_info *p_var;
struct att_info *p_att;
int var_id; /* netCDF ID for variable */
char *signstr;
nc_type nctype;
old_ncopts =get_ncopts();
set_ncopts(0);
fd = micreate(path, NC_CLOBBER);
set_ncopts(old_ncopts);
if (fd < 0) {
return (MINC_STATUS_ERROR);
}
if (ct > 0) {
dim_id[MI_S_T] = ncdimdef(fd, MItime, ct);
micreate_std_variable(fd, MItime, NC_INT, 0, NULL);
if (dt > 0.0) {
miattputdbl(fd, ncvarid(fd, MItime), MIstep, dt);
}
}
else {
dim_id[MI_S_T] = -1;
}
if (cz > 0) {
dim_id[MI_S_Z] = ncdimdef(fd, MIzspace, cz);
micreate_std_variable(fd, MIzspace, NC_INT, 0, NULL);
if (dz > 0.0) {
miattputdbl(fd, ncvarid(fd, MIzspace), MIstep, dz);
}
}
else {
dim_id[MI_S_Z] = -1;
}
if (cy > 0) {
dim_id[MI_S_Y] = ncdimdef(fd, MIyspace, cy);
micreate_std_variable(fd, MIyspace, NC_INT, 0, NULL);
if (dy > 0.0) {
miattputdbl(fd, ncvarid(fd, MIyspace), MIstep, dy);
}
}
else {
return (MINC_STATUS_ERROR); /* Must define Y */
}
if (cx > 0) {
dim_id[MI_S_X] = ncdimdef(fd, MIxspace, cx);
micreate_std_variable(fd, MIxspace, NC_INT, 0, NULL);
if (dx > 0.0) {
miattputdbl(fd, ncvarid(fd, MIxspace), MIstep, dx);
}
}
else {
return (MINC_STATUS_ERROR); /* Must define X */
}
/* The var_dims[] array is the array of actual dimension ID's to
* be used in defining the image variables. Here I set it up by
* copying all valid dimension ID's from the dim_id[] array.
*/
var_ndims = 0;
for (i = 0; i < MI_S_NDIMS; i++) {
if (dim_id[i] >= 0) {
var_dims[var_ndims] = dim_id[i];
var_ndims++;
}
}
minc_simple_to_nc_type(filetype, &nctype, &signstr);
/* Create the image variable with the standard
* dimension order, and the same type as the template
* file.
*/
micreate_std_variable(fd, MIimage, nctype, var_ndims, var_dims);
micreate_std_variable(fd, MIimagemin, NC_DOUBLE, 1, var_dims);
micreate_std_variable(fd, MIimagemax, NC_DOUBLE, 1, var_dims);
/* Copy information from the infoptr to the output.
*/
if ((p_file = infoptr) != NULL) {
old_ncopts =get_ncopts();
set_ncopts(0);
for (i = 0; i < p_file->file_natts; i++) {
p_att = &p_file->file_atts[i];
if (strcmp(p_att->att_name, "ident") != 0) {
ncattput(fd, NC_GLOBAL, p_att->att_name, p_att->att_type,
p_att->att_len, p_att->att_val);
}
}
for (i = 0; i < p_file->file_nvars; i++) {
p_var = &p_file->file_vars[i];
if ((var_id = ncvarid(fd, p_var->var_name)) < 0) {
var_id = ncvardef(fd, p_var->var_name, p_var->var_type,
p_var->var_ndims, p_var->var_dims);
}
for (j = 0; j < p_var->var_natts; j++) {
p_att = &p_var->var_atts[j];
ncattput(fd, var_id, p_att->att_name, p_att->att_type,
p_att->att_len, p_att->att_val);
}
}
set_ncopts(old_ncopts);
}
miattputstr(fd, ncvarid(fd, MIimage), MIcomplete, MI_FALSE);
miattputstr(fd, ncvarid(fd, MIimage), MIsigntype, signstr);
miappend_history(fd, history);
ncendef(fd);
return fd;
}
/* Test case 1 - file creation & definition.
*/
static int test1(struct testinfo *ip, struct dimdef *dims, int ndims)
{
int varid;
int stat;
int i;
/* Test case #1 - file creation
*/
ip->name = micreate_tempfile();
if (ip->name == NULL) {
FUNC_ERROR("micreate_tempfile\n");
}
ip->fd = micreate(ip->name, NC_CLOBBER);
if (ip->fd < 0) {
FUNC_ERROR("micreate");
}
/* Have to use ncdimdef() here since there is no MINC equivalent. Sigh.
*/
for (i = 0; i < ndims; i++) {
/* Define the dimension
*/
ip->dim[i] = ncdimdef(ip->fd, dims[i].name, dims[i].length);
if (ip->dim[i] < 0) {
FUNC_ERROR("ncdimdef");
}
/* Create the dimension variable.
*/
varid = micreate_std_variable(ip->fd, dims[i].name, NC_DOUBLE, 0,
&ip->dim[i]);
if (varid < 0) {
FUNC_ERROR("micreate_std_variable");
}
stat = miattputdbl(ip->fd, varid, MIstep, 0.8);
if (stat < 0) {
FUNC_ERROR("miattputdbl");
}
stat = miattputdbl(ip->fd, varid, MIstart, 22.0);
if (stat < 0) {
FUNC_ERROR("miattputdbl");
}
}
/* Create the image-max variable.
*/
ip->maxid = micreate_std_variable(ip->fd, MIimagemax, NC_FLOAT, 0, NULL);
if (ip->maxid < 0) {
FUNC_ERROR("micreate_std_variable");
}
/* Create the image-min variable.
*/
ip->minid = micreate_std_variable(ip->fd, MIimagemin, NC_FLOAT, 0, NULL);
if (ip->minid < 0) {
FUNC_ERROR("micreate_std_variable");
}
ip->imgid = micreate_std_variable(ip->fd, MIimage, NC_INT, ndims, ip->dim);
if (ip->imgid < 0) {
FUNC_ERROR("micreate_std_variable");
}
ip->test_group = ncvardef(ip->fd,(char*)"test",NC_INT,0,0);/* micreate_group_variable(ip->fd,(char*)"test");*/
if(ip->test_group<0)
{
FUNC_ERROR("micreate_group_variable");
}
ip->large_attribute=calloc(ip->attribute_size,sizeof(char));
memset(ip->large_attribute,'X',ip->attribute_size-1);
ip->test_attribute = ncattput(ip->fd, ip->test_group, "test", NC_CHAR, ip->attribute_size, ip->large_attribute);
return (0);
}
/* Test case 1 - file creation & definition.
*/
int
test1(struct testinfo *ip, struct dimdef *dims, int ndims)
{
int fd2;
int varid;
int stat;
int i;
/* Test case #1 - file creation
*/
ip->name = micreate_tempfile();
if (ip->name == NULL) {
FUNC_ERROR("micreate_tempfile\n");
}
ip->fd = micreate(ip->name, NC_CLOBBER);
if (ip->fd < 0) {
FUNC_ERROR("micreate");
}
/* Try to create another file of the same name - should fail.
*/
fd2 = micreate(ip->name, NC_NOCLOBBER);
if (fd2 >= 0) {
FUNC_ERROR("micreate");
}
/* Try to open the file for write - should fail.
*/
/* VF: it doesn't fail!
fd2 = miopen(ip->name, NC_WRITE);
if (fd2 >= 0) {
FUNC_ERROR("miopen");
} */
/* Have to use ncdimdef() here since there is no MINC equivalent. Sigh.
*/
for (i = 0; i < ndims; i++) {
/* Define the dimension
*/
ip->dim[i] = ncdimdef(ip->fd, dims[i].name, dims[i].length);
if (ip->dim[i] < 0) {
FUNC_ERROR("ncdimdef");
}
/* Create the dimension variable.
*/
varid = micreate_std_variable(ip->fd, dims[i].name, NC_DOUBLE, 0,
&ip->dim[i]);
if (varid < 0) {
FUNC_ERROR("micreate_std_variable");
}
stat = miattputdbl(ip->fd, varid, MIstep, 0.8);
if (stat < 0) {
FUNC_ERROR("miattputdbl");
}
stat = miattputdbl(ip->fd, varid, MIstart, 22.0);
if (stat < 0) {
FUNC_ERROR("miattputdbl");
}
}
/* Try to create a bogus variable. This should trigger an error.
*/
varid = micreate_std_variable(ip->fd, "xyzzy", NC_DOUBLE, 0, NULL);
if (varid >= 0) {
FUNC_ERROR("micreate_std_variable");
}
/* Create the image-max variable.
*/
ip->maxid = micreate_std_variable(ip->fd, MIimagemax, NC_FLOAT, 0, NULL);
if (ip->maxid < 0) {
FUNC_ERROR("micreate_std_variable");
}
/* Create the image-min variable.
*/
ip->minid = micreate_std_variable(ip->fd, MIimagemin, NC_FLOAT, 0, NULL);
if (ip->minid < 0) {
FUNC_ERROR("micreate_std_variable");
}
ip->imgid = micreate_std_variable(ip->fd, MIimage, NC_INT, ndims, ip->dim);
if (ip->imgid < 0) {
FUNC_ERROR("micreate_std_variable");
}
return (0);
}
int
upet_to_minc(char *hdr_fname, char *img_fname, char *out_fname,
char *prog_name)
{
char *line_ptr;
char line_buf[1024];
char *val_ptr;
int in_header;
double dbl_tmp;
int int_tmp;
struct conversion_info ci;
struct keywd_entry *ke_ptr;
int is_known;
char *argv_tmp[5];
char *out_history;
ci.hdr_fp = fopen(hdr_fname, "r"); /* Text file */
if (ci.hdr_fp == NULL) {
perror(hdr_fname);
return (-1);
}
ci.img_fp = fopen(img_fname, "rb"); /* Binary file */
if (ci.img_fp == NULL) {
perror(img_fname);
return (-1);
}
ci.mnc_fd = micreate(out_fname, NC_NOCLOBBER);
if (ci.mnc_fd < 0) {
perror(out_fname);
return (-1);
}
ci.frame_zero = -1; /* Initial frame is -1 until set. */
/* Define the basic MINC group variables.
*/
micreate_group_variable(ci.mnc_fd, MIstudy);
micreate_group_variable(ci.mnc_fd, MIacquisition);
micreate_group_variable(ci.mnc_fd, MIpatient);
ncvardef(ci.mnc_fd, "micropet", NC_SHORT, 0, NULL);
/* Fake the history here */
argv_tmp[0] = prog_name;
argv_tmp[1] = VERSIONSTR;
argv_tmp[2] = hdr_fname;
argv_tmp[3] = img_fname;
argv_tmp[4] = out_fname;
out_history = time_stamp(5, argv_tmp);
miattputstr(ci.mnc_fd, NC_GLOBAL, MIhistory, out_history);
free(out_history);
in_header = 1;
ci.frame_nbytes = 1;
ci.frame_nvoxels = 1;
/* When we read voxels, we need COMBINED_SCALE_FACTOR() to have a sane
* value for all modalities. Set defaults for these in case the modality
* does not define one of these factors. For example, a CT (modality 2)
* will not define isotope_branching_fraction or calibration_factor.
*/
ci.scale_factor = 1.0;
ci.calibration_factor = 1.0;
ci.isotope_branching_fraction = 1.0;
/* Collect the headers */
while (fgets(line_buf, sizeof(line_buf), ci.hdr_fp) != NULL) {
if (line_buf[0] == '#') /* */
continue;
line_ptr = line_buf;
while (!isspace(*line_ptr)) {
line_ptr++;
}
*line_ptr++ = '\0';
val_ptr = line_ptr;
while (*line_ptr != '\n' && *line_ptr != '\r' && *line_ptr != '\0') {
line_ptr++;
}
*line_ptr = '\0';
is_known = 0;
if (in_header) {
if (*val_ptr != '\0') {
/* Save the raw attribute into the file */
ncattput(ci.mnc_fd, ncvarid(ci.mnc_fd, "micropet"),
line_buf, NC_CHAR, strlen(val_ptr), val_ptr);
}
for (ke_ptr = vol_atts; ke_ptr->upet_kwd != NULL; ke_ptr++) {
if (!strcmp(ke_ptr->upet_kwd, line_buf)) {
is_known = 1;
if (ke_ptr->func != NULL) {
(*ke_ptr->func)(&ci, val_ptr,
ke_ptr->mnc_var,
ke_ptr->mnc_att);
}
else if (ke_ptr->mnc_var != NULL &&
ke_ptr->mnc_att != NULL) {
/* Interpret based upon type */
switch (ke_ptr->upet_type) {
case UPET_TYPE_INT:
int_tmp = atoi(val_ptr);
miattputint(ci.mnc_fd,
ncvarid(ci.mnc_fd, ke_ptr->mnc_var),
ke_ptr->mnc_att,
int_tmp);
break;
case UPET_TYPE_REAL:
dbl_tmp = atof(val_ptr);
miattputdbl(ci.mnc_fd,
ncvarid(ci.mnc_fd, ke_ptr->mnc_var),
ke_ptr->mnc_att,
dbl_tmp);
break;
case UPET_TYPE_STR:
miattputstr(ci.mnc_fd,
ncvarid(ci.mnc_fd, ke_ptr->mnc_var),
ke_ptr->mnc_att,
val_ptr);
break;
}
}
break;
}
}
}
else {
/* Not in the header any longer
*/
for (ke_ptr = frm_atts; ke_ptr->upet_kwd != NULL; ke_ptr++) {
if (!strcmp(ke_ptr->upet_kwd, line_buf)) {
is_known = 1;
if (ke_ptr->func != NULL) {
(*ke_ptr->func)(&ci, val_ptr,
ke_ptr->mnc_var,
ke_ptr->mnc_att);
}
break;
}
}
}
if (!is_known) {
if (!strcmp(line_buf, "end_of_header")) {
if (in_header) {
in_header = 0;
copy_init(&ci);
}
else {
copy_frame(&ci);
}
}
else {
message(MSG_WARNING, "Unrecognized keyword %s\n", line_buf);
}
}
}
fclose(ci.hdr_fp);
fclose(ci.img_fp);
miclose(ci.mnc_fd);
return (0);
}
