int main(int argc, char *argv[])
{
char history[STRINGLENGTH];
int result,i;
long n3,n2,n1;
mihandle_t inputfile, outputfile;
double step3, step2, step1;
double start3, start2, start1;
double starts[3], separations[3];
history[0]='\0';
if(argc!=3)
{
fprintf(stderr, "Usage: input file and an output file!\n");
return 1;
}
if (argc > 1)
{
for (i=0;i<argc;i++)
{
strcat(history, argv[i]);
strcat(history," ");
}
}
result = open_minc_file_and_read(argv[1], &inputfile);
if(result) { return 1; }
result = get_minc_spatial_dimensions_from_handle(inputfile, &n3, &n2, &n1);
if(result) { return 1; }
result = get_minc_spatial_separations_from_handle(inputfile, &step3,&step2,&step1);
if(result) { return 1; }
result = get_minc_spatial_starts_from_handle(inputfile, &start3,&start2,&start1);
if(result) { return 1; }
starts[0] = start3;
starts[1] = start2;
starts[2] = start1;
separations[0] = step3;
separations[1] = step2;
separations[2] = step1;
result = open_minc_file_and_write(argv[2], &outputfile, n3, n2, n1, starts, separations,COMPLEX);
if(result) { return 1; }
result = miadd_history_attr(outputfile, strlen(history), history);
if(result) {printf("could not history to minc header!!!\n");}
result = micopy_attr(inputfile,"/OPT",outputfile);
if(result) {printf("could not copy attributes at path /OPT or does not exist\n");}
result = threedifft(inputfile, outputfile, n3, n2, n1);
if(result) { return 1;}
result = miclose_volume(inputfile);
if(result) { return 1;}
result = miclose_volume(outputfile);
if(result) { return 1;}
return 0;
}
SEXP minc_overwrite_history(SEXP filename, SEXP history, SEXP hist_size){
const char *history_line = CHAR(asChar(history));
const char *filepath = CHAR(asChar(filename));
int history_size = asInteger(hist_size);
mihandle_t hvol;
int read_result;
int hist_edit_result;
read_result = miopen_volume(filepath,
MI2_OPEN_RDWR, &hvol);
if (read_result != MI_NOERROR) {
error("Error opening input file: %s.\n", filepath);
}
hist_edit_result = miadd_history_attr(hvol, history_size, history_line);
if(hist_edit_result != MI_NOERROR){
error("Error editing history for file: %s \n", filepath);
}
miclose_volume(hvol);
return(R_NilValue);
}
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);
}
