SEXP get_minc_separations(SEXP filename) {
int result;
mihandle_t hvol;
const char *filepath = CHAR(asChar(filename));
midimhandle_t dimensions[3];
double* voxel_separations = malloc(3 * sizeof(double));
SEXP output = PROTECT(allocVector(REALSXP, 3));
result = miopen_volume(filepath,
MI2_OPEN_READ, &hvol);
if (result != MI_NOERROR) {
miclose_volume(hvol);
error("Error opening input file: %s.\n", filepath);
}
result =
miget_volume_dimensions(hvol, MI_DIMCLASS_SPATIAL, MI_DIMATTR_ALL,
MI_DIMORDER_FILE, 3, dimensions);
result =
miget_dimension_separations(dimensions, MI_ORDER_FILE,
3, voxel_separations);
miclose_volume(hvol);
for(int i = 0; i < 3; ++i) REAL(output)[i] = voxel_separations[i];
UNPROTECT(1);
return(output);
}
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;
}
void get_volume_sizes(char **filename, unsigned int *sizes) {
int result;
mihandle_t hvol;
misize_t tmp_sizes[3];
midimhandle_t dimensions[3];
/* open the existing volume */
result = miopen_volume(filename[0],
MI2_OPEN_READ, &hvol);
if (result != MI_NOERROR) {
error("Error opening input file: %s.\n", filename[0]);
}
/* get the file dimensions and their sizes */
miget_volume_dimensions( hvol, MI_DIMCLASS_SPATIAL,
MI_DIMATTR_ALL, MI_DIMORDER_FILE,
3, dimensions);
result = miget_dimension_sizes( dimensions, 3, tmp_sizes );
//Rprintf("Sizes: %i %i %i\n", tmp_sizes[0], tmp_sizes[1], tmp_sizes[2]);
sizes[0] = (unsigned int) tmp_sizes[0];
sizes[1] = (unsigned int) tmp_sizes[1];
sizes[2] = (unsigned int) tmp_sizes[2];
// Close the volume, to free handle
result = miclose_volume(hvol);
if (result != MI_NOERROR) {
error("Error closing file: %s.\n", filename[0]);
}
return;
}
/* get a voxel from all files, world coordinates */
void get_world_voxel_from_files(char **filenames, int *num_files,
double *v1, double *v2, double *v3,
double *voxel) {
double location[3], voxel_coord_tmp[3];
misize_t voxel_coord[3];
mihandle_t hvol;
int result;
int i, j;
location[0] = *v1;
location[1] = *v2;
location[2] = *v3;
for(i=0; i < *num_files; i++) {
/* open the volume */
result = miopen_volume(filenames[i],
MI2_OPEN_READ, &hvol);
if (result != MI_NOERROR) {
error("Error opening input file: %s.\n", filenames[i]);
}
miconvert_world_to_voxel(hvol, location, voxel_coord_tmp);
for (j=0; j < 3; j++) {
voxel_coord[j] = (unsigned long) voxel_coord_tmp[j] + 0.5;
}
result = miget_real_value(hvol, voxel_coord, 3, &voxel[i]);
if (result != MI_NOERROR) {
error("Error getting voxel from: %s.\n", filenames[i]);
}
miclose_volume(hvol);
}
}
/* get a voxel from all files, voxel coordinates */
void get_voxel_from_files(char **filenames, int *num_files,
int *v1, int *v2, int *v3, double *voxel) {
misize_t location[3];
mihandle_t hvol;
int result;
int i;
location[0] = *v1;
location[1] = *v2;
location[2] = *v3;
for(i=0; i < *num_files; i++) {
/* open the volume */
result = miopen_volume(filenames[i],
MI2_OPEN_READ, &hvol);
if (result != MI_NOERROR) {
error("Error opening input file: %s.\n", filenames[i]);
}
result = miget_real_value(hvol, location, 3, &voxel[i]);
if (result != MI_NOERROR) {
error("Error getting voxel from: %s.\n", filenames[i]);
}
miclose_volume(hvol);
}
}
void free_minc_files(SEXP filenames, mihandle_t *hvol) {
int num_files, i;
num_files = LENGTH(filenames);
for (i=0; i < num_files; i++) {
miclose_volume(hvol[i]);
//free
}
}
void create_test_file(void)
{
int r;
double start_values[3]= {-6.96, -12.453, -9.48};
double separations[3]= {0.09,0.09,0.09};
midimhandle_t hdim[NDIMS];
mihandle_t hvol;
unsigned short *buf = ( unsigned short *) malloc(CX * CY * CZ * sizeof(unsigned short));
int i;
long count[NDIMS];
long start[NDIMS];
miboolean_t flag=1;
double min = -1.0;
double max = 1.0;
r = micreate_dimension("zspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CZ, &hdim[0]);
r = micreate_dimension("yspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CY, &hdim[1]);
r = micreate_dimension("xspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CX, &hdim[2]);
r = miset_dimension_starts(hdim, NDIMS, start_values);
r = miset_dimension_separations(hdim, NDIMS, separations);
r = micreate_volume("hyperslab-test2.mnc", NDIMS, hdim, MI_TYPE_USHORT,
MI_CLASS_REAL, NULL, &hvol);
/* set slice scaling flag to true */
r = miset_slice_scaling_flag(hvol, flag);
r = micreate_volume_image(hvol);
for (i = 0; i < CZ*CY*CX; i++) {
buf[i] = (unsigned short) i * 0.01;
}
start[0] = start[1] = start[2] = 0;
count[0] = CZ;
count[1] = CY;
count[2] = CX;
r = miset_voxel_value_hyperslab(hvol, MI_TYPE_USHORT, start, count, buf);
/* Set random values to slice min and max for slice scaling*/
start[0] =start[1]=start[2]=0;
for (i=0; i < CZ; i++) {
start[0] = i;
min += 0.1;
max += 0.1;
r = miset_slice_range(hvol,start, 3, max, min);
}
r = miclose_volume(hvol);
}
SEXP get_minc_history(SEXP filename) {
int result;
mihandle_t hvol;
int int_size = asInteger(minc_history_size(filename));
char *history = malloc(int_size);
const char *filepath = CHAR(asChar(filename));
result = miopen_volume(filepath,
MI2_OPEN_READ, &hvol);
if (result != MI_NOERROR) {
miclose_volume(hvol);
error("Error opening input file: %s.\n", filepath);
}
miget_attr_values(hvol, MI_TYPE_STRING, "", "history", int_size, history);
miclose_volume(hvol);
SEXP output = PROTECT(mkString(history));
free(history);
UNPROTECT(1);
return(output);
}
int create_2D_image(void)
{
int r,i;
midimhandle_t hdim[NDIMS-1];
mihandle_t hvol;
short *buf = (short *)malloc(CX * CY * sizeof(short));
double *offsets = (double *)malloc(CX * sizeof(double));
double start_values[NDIMS-1]={-1.01, -2.02};
miboolean_t flag=0;
long count[NDIMS-1];
long start[NDIMS-1];
r = micreate_dimension("xspace", MI_DIMCLASS_SPATIAL, MI_DIMATTR_NOT_REGULARLY_SAMPLED, CX, &hdim[0]);
r = micreate_dimension("yspace", MI_DIMCLASS_USER, MI_DIMATTR_REGULARLY_SAMPLED, CY, &hdim[1]);
for(i=0; i < CX; i++)
{
offsets[i] = (i * i) + 0.1;
}
r = miset_dimension_offsets(hdim[0], CX, 0, offsets);
r = miset_dimension_separation(hdim[1], 0.06);
r = miset_dimension_starts(hdim, NDIMS-1, start_values);
r = micreate_volume("2D_image.mnc", NDIMS-1 , hdim, MI_TYPE_SHORT,
MI_CLASS_REAL, NULL, &hvol);
/* set slice scaling flag to true */
r = miset_slice_scaling_flag(hvol, flag);
r = micreate_volume_image(hvol);
for (i = 0; i < CX*CY; i++) {
buf[i] = (short) i * 0.1;
}
start[0] = start[1] = 0;
count[0] = CX; count[1] = CY;
r = miset_voxel_value_hyperslab(hvol, MI_TYPE_SHORT, start, count, buf);
r = miclose_volume(hvol);
return r<0?1:0;
}
int
main(int argc, char **argv)
{
miclass_t myclass = MI_CLASS_REAL;
mitype_t mytype = MI_TYPE_UNKNOWN;
misize_t mysize = 0;
char *myname = NULL;
mihandle_t volume = NULL;
/* Turn off automatic error reporting.
*/
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
/* Check each file.
*/
while (--argc > 0) {
++argv;
if (micreate_volume(*argv, 0, NULL, MI_TYPE_INT, 0, NULL, &volume) < 0) { /*type 0 is equivalent to H5T_INTEGER */
fprintf(stderr, "Error opening %s\n", *argv);
}
else {
int i;
/* Repeat many times to expose resource leakage problems, etc.
*/
for (i = 0; i < 25000; i++) {
miget_data_type(volume, &mytype);
miget_data_type_size(volume, &mysize);
miget_data_class(volume, &myclass);
miget_space_name(volume, &myname);
mifree_name(myname);
}
miclose_volume(volume);
printf("file: %s type %d size %lld class %d\n", *argv,
mytype, mysize, myclass);
}
}
return (0);
}
/* convert voxel coordinates to a vector of world coords */
void convert_voxel_to_world(char **filenames, double *v1, double *v2,
double *v3, double *world_coords) {
int result;
mihandle_t hvol;
double voxel_coords[3];
/* open the volume */
result = miopen_volume(filenames[0], MI2_OPEN_READ, &hvol);
if (result != MI_NOERROR) {
error("Error opening input file: %s.\n", filenames[0]);
}
voxel_coords[0] = *v1;
voxel_coords[1] = *v2;
voxel_coords[2] = *v3;
miconvert_voxel_to_world(hvol, voxel_coords, world_coords);
miclose_volume(hvol);
}
SEXP get_vector_from_files(SEXP filenames, SEXP num_files, SEXP vec_length,
SEXP v1, SEXP v2, SEXP v3) {
misize_t location[4];
mihandle_t hvol;
int result;
int i, j, vector_length, number_files;
SEXP output;
double *xoutput;
vector_length = *INTEGER(vec_length);
number_files = *INTEGER(num_files);
location[1] = *INTEGER(v1);
location[2] = *INTEGER(v2);
location[3] = *INTEGER(v3);
Rprintf("NFILES: %d NVEC: %d\n", number_files, vector_length);
PROTECT(output=allocMatrix(REALSXP, number_files, vector_length));
xoutput = REAL(output);
for(i=0; i < number_files; i++) {
/* open the volume */
result = miopen_volume(CHAR(STRING_ELT(filenames,i)),
MI2_OPEN_READ, &hvol);
if (result != MI_NOERROR) {
error("Error opening input file: %s.\n", CHAR(STRING_ELT(filenames, i)));
}
for(j=0; j < vector_length; j++) {
location[0] = j;
result = miget_real_value(hvol, location, 4, &xoutput[i + number_files*j]);
if (result != MI_NOERROR) {
error("Error getting voxel from: %s.\n", CHAR(STRING_ELT(filenames, i)));
}
}
miclose_volume(hvol);
}
UNPROTECT(1);
return(output);
}
SEXP minc_history_size(SEXP filename){
size_t hist_size;
mihandle_t hvol;
int result;
const char *filepath = CHAR(asChar(filename));
result = miopen_volume(filepath,
MI2_OPEN_READ, &hvol);
if (result != MI_NOERROR) {
error("Error opening input file: %s.\n", filepath);
}
miget_attr_length(hvol, "", "history", &hist_size);
miclose_volume(hvol);
SEXP output = ScalarInteger((int) hist_size);
return(output);
}
int main ( int argc, char **argv )
{
mihandle_t hvol;
int r;
misize_t coords[3];
double min, max;
int i;
while ( --argc > 0 ) {
const char *fname=*++argv;
printf("Checking %s\n",fname);
r = miopen_volume ( fname, MI2_OPEN_READ, &hvol );
if ( r < 0 ) {
fprintf ( stderr, "can't open %s, error %d\n", *argv, r );
return 1;
} else {
for ( i = 0; i < CZ; i++ ) {
coords[0] = i; /*Z*/
coords[1] = rand()%CX; /*X*/
coords[2] = rand()%CY; /*Y*/
r = miget_slice_min ( hvol, coords, 3, &min );
if ( r < 0 ) {
fprintf ( stderr, "error %d getting slice minimum at %d %d %d\n", r, (int)coords[0],(int)coords[1],(int)coords[2] );
return 1;
}
r = miget_slice_max ( hvol, coords, 3, &max );
if ( r < 0 ) {
fprintf ( stderr, "error %d getting slice maximum at %d %d %d\n", r,(int)coords[0],(int)coords[1],(int)coords[2] );
return 1;
}
/*printf ( "%d. min %f max %f\n", i, min, max );*/
/*PASS*/
}
miclose_volume ( hvol );
}
}
return ( 0 );
}
static void create_test_file ( void )
{
midimhandle_t hdim[NDIMS];
mihandle_t hvol;
unsigned char *buf = malloc ( CZ * CX * CY * 3 );
int i;
misize_t count[NDIMS];
misize_t start[NDIMS];
micreate_dimension ( "zspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CZ, &hdim[0] );
micreate_dimension ( "yspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CY, &hdim[1] );
micreate_dimension ( "xspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CX, &hdim[2] );
micreate_dimension ( "vector_dimension", MI_DIMCLASS_RECORD,
MI_DIMATTR_REGULARLY_SAMPLED, 3, &hdim[3] );
micreate_volume ( "example_vector2.mnc", NDIMS, hdim, MI_TYPE_BYTE,
MI_CLASS_INT, NULL, &hvol );
micreate_volume_image ( hvol );
for ( i = 0; i < CZ * CY * CX * 3; i++ ) {
buf[i] = ( unsigned char ) i;
}
start[0] = start[1] = start[2] = start[3] = 0;
count[0] = CZ;
count[1] = CY;
count[2] = CX;
count[3] = 3;
miset_voxel_value_hyperslab ( hvol, MI_TYPE_BYTE, start, count, buf );
miclose_volume ( hvol );
}
/* get a real value hyperslab from file */
void get_hyperslab(char **filename, int *start, int *count, double *slab) {
int result;
mihandle_t hvol;
int i;
unsigned long tmp_start[3];
unsigned long tmp_count[3];
/* open the volume */
result = miopen_volume(filename[0],
MI2_OPEN_READ, &hvol);
if (result != MI_NOERROR) {
error("Error opening input file: %s.\n", filename[0]);
}
for (i=0; i < 3; i++) {
tmp_start[i] = (unsigned long) start[i];
tmp_count[i] = (unsigned long) count[i];
}
/* get the hyperslab */
//Rprintf("Start: %i %i %i\n", start[0], start[1], start[2]);
//Rprintf("Count: %i %i %i\n", count[0], count[1], count[2]);
if (miget_real_value_hyperslab(hvol,
MI_TYPE_DOUBLE,
(misize_t *) tmp_start,
(misize_t *) tmp_count,
slab)
< 0) {
error("Could not get hyperslab.\n");
}
// Close the volume, to free handle
result = miclose_volume(hvol);
if (result != MI_NOERROR) {
error("Error closing file: %s.\n", filename[0]);
}
return;
}
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);
}
vector<mihandle_t> open_minc2_volumes(CharacterVector filenames){
vector<mihandle_t> volumes;
mihandle_t current_handle;
CharacterVector::iterator file_iterator;
vector<mihandle_t>::iterator volume_iterator;
for(file_iterator = filenames.begin();
file_iterator != filenames.end();
++file_iterator){
try {
current_handle = open_minc2_volume(wrap(*file_iterator));
} catch(...){
for(volume_iterator = volumes.begin(); volume_iterator != volumes.end(); ++volume_iterator){
miclose_volume(*volume_iterator);
}
throw;
}
volumes.push_back(current_handle);
}
return(volumes);
}
int main(void)
{
mihandle_t vol;
int r;
midimhandle_t dim[NDIMS];
int n;
misize_t coords[NDIMS];
misize_t count[NDIMS];
int i,j,k;
double offset;
unsigned int voxel;
/* Write data one voxel at a time. */
for (i = 0; i < NDIMS; i++) {
count[i] = 1;
}
r = micreate_dimension("time", MI_DIMCLASS_TIME,
MI_DIMATTR_NOT_REGULARLY_SAMPLED, CT, &dim[0]);
if (r < 0) {
TESTRPT("failed", r);
}
for (i = 0; i < CT; i++) {
offset = (i * i) + 100.0;
r = miset_dimension_offsets(dim[0], 1, i, &offset);
if (r < 0) {
TESTRPT("failed", r);
}
}
r = micreate_dimension("xspace",MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CX, &dim[1]);
if (r < 0) {
TESTRPT("failed", r);
}
r = miset_dimension_start(dim[1], XSTART);
if (r < 0) {
TESTRPT("failed", r);
}
r = miset_dimension_separation(dim[1], XSTEP);
if (r < 0) {
TESTRPT("failed", r);
}
r = micreate_dimension("yspace",MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CY, &dim[2]);
if (r < 0) {
TESTRPT("failed", r);
}
r = miset_dimension_start(dim[2], YSTART);
if (r < 0) {
TESTRPT("failed", r);
}
r = miset_dimension_separation(dim[2], YSTEP);
if (r < 0) {
TESTRPT("failed", r);
}
r = micreate_dimension("zspace",MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CZ, &dim[3]);
if (r < 0) {
TESTRPT("failed", r);
}
r = miset_dimension_start(dim[3], ZSTART);
if (r < 0) {
TESTRPT("failed", r);
}
r = miset_dimension_separation(dim[3], ZSTEP);
if (r < 0) {
TESTRPT("failed", r);
}
r = micreate_volume("tst-dim.mnc", NDIMS, dim, MI_TYPE_UINT,
MI_CLASS_REAL, NULL, &vol);
if (r < 0) {
TESTRPT("failed", r);
}
r = micreate_volume_image(vol);
if (r < 0) {
TESTRPT("failed", r);
}
check_dims(vol, dim);
for (i = 0; i < CX; i++) {
for (j = 0; j < CY; j++) {
for (k = 0; k < CZ; k++) {
coords[0] = 0;
coords[1] = i;
coords[2] = j;
coords[3] = k;
voxel = (i*10000)+(j*100)+k;
r = miset_voxel_value_hyperslab(vol,
MI_TYPE_UINT,
coords,
count,
&voxel);
if (r < 0) {
TESTRPT("Error writing voxel", r);
}
}
}
}
r = miclose_volume(vol);
if (r < 0) {
TESTRPT("failed", r);
}
/***** 03-Aug-2004: Added two tests for bugs reported by Leila */
r = miopen_volume("tst-dim.mnc", MI2_OPEN_RDWR, &vol);
if (r < 0) {
TESTRPT("failed", r);
}
r = miget_volume_dimension_count(vol, MI_DIMCLASS_ANY,
MI_DIMATTR_REGULARLY_SAMPLED, &n);
if (r < 0) {
TESTRPT("failed", r);
}
if (n != NDIMS - 1) {
TESTRPT("wrong result", n);
}
r = miget_volume_dimension_count(vol, MI_DIMCLASS_ANY,
MI_DIMATTR_NOT_REGULARLY_SAMPLED, &n);
if (r < 0) {
TESTRPT("failed", r);
}
if (n != 1) {
TESTRPT("wrong result", n);
}
r = miclose_volume(vol);
if (r < 0) {
TESTRPT("failed", r);
}
/* Test #2 - verify that we don't print anything scary if a user
* closes a volume prematurely.
*/
r = micreate_dimension("xspace",MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CX, &dim[0]);
if (r < 0) {
TESTRPT("failed", r);
}
r = micreate_dimension("yspace",MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CY, &dim[1]);
if (r < 0) {
TESTRPT("failed", r);
}
r = micreate_dimension("zspace",MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CZ, &dim[2]);
if (r < 0) {
TESTRPT("failed", r);
}
r = micreate_volume("tst-vol.mnc", 3, dim, MI_TYPE_SHORT,
MI_CLASS_LABEL, NULL, &vol);
if (r < 0) {
TESTRPT("failed", r);
}
r = miclose_volume(vol);
if (r < 0) {
TESTRPT("failed", r);
}
/** End of tests added 03-Aug-2004 **/
if (error_cnt != 0) {
fprintf(stderr, "%d error%s reported\n",
error_cnt, (error_cnt == 1) ? "" : "s");
}
else {
fprintf(stderr, "No errors\n");
}
return (error_cnt);
}
int main(int argc, char **argv)
{
mihandle_t vol;
int r;
midimhandle_t dim[NDIMS];
mivolumeprops_t props;
int n;
unsigned long coords[NDIMS];
unsigned long count[NDIMS];
int i,j,k;
unsigned int voxel;
printf("Creating volume...\n");
/* Write data one voxel at a time. */
for (i = 0; i < NDIMS; i++) {
count[i] = 1;
}
r = minew_volume_props(&props);
r = miset_props_compression_type(props, MI_COMPRESS_ZLIB);
r = miset_props_zlib_compression(props, 3);
r = miset_props_multi_resolution(props, 1, 3);
if (r < 0) {
TESTRPT("failed", r);
}
r = micreate_dimension("xspace",MI_DIMCLASS_SPATIAL,MI_DIMATTR_REGULARLY_SAMPLED, CX,&dim[0]);
if (r < 0) {
TESTRPT("failed", r);
}
r = micreate_dimension("yspace",MI_DIMCLASS_SPATIAL,MI_DIMATTR_REGULARLY_SAMPLED, CY, &dim[1]);
if (r < 0) {
TESTRPT("failed", r);
}
r = micreate_dimension("zspace",MI_DIMCLASS_SPATIAL,MI_DIMATTR_REGULARLY_SAMPLED, CZ,&dim[2]);
if (r < 0) {
TESTRPT("failed", r);
}
r = micreate_volume("tst-multi.mnc", NDIMS, dim, MI_TYPE_UINT, MI_CLASS_REAL,props,&vol);
if (r < 0) {
TESTRPT("failed", r);
}
r = miset_volume_valid_range(vol, CX*10000.0 + CY*100 + CZ, 0.0);
r = micreate_volume_image(vol);
if (r < 0) {
TESTRPT("failed", r);
}
r = miget_volume_dimension_count(vol, MI_DIMCLASS_SPATIAL, MI_DIMATTR_ALL, &n);
if (r < 0) {
TESTRPT("failed", r);
}
printf("Writing data...\n");
for (i = 0; i < CX; i++) {
for (j = 0; j < CY; j++) {
for (k = 0; k < CZ; k++) {
coords[0] = i;
coords[1] = j;
coords[2] = k;
voxel = i*10000 + j*100 + k;
r = miset_voxel_value_hyperslab(vol, MI_TYPE_UINT,
coords, count, &voxel);
if (r < 0) {
TESTRPT("Error writing voxel", r);
}
}
}
}
printf("Selecting half-size image\n");
r = miselect_resolution(vol, 1);
if (r < 0) {
TESTRPT("miselect_resolution failed", r);
}
/* OK, now try to read the lower-resolution hyperslab */
coords[0] = 0;
coords[1] = 0;
coords[2] = 0;
count[0] = CX/2;
count[1] = CY/2;
count[2] = CZ/2;
{
unsigned int buffer[CX/2][CY/2][CZ/2];
r = miget_voxel_value_hyperslab(vol, MI_TYPE_UINT,
coords, count, buffer);
if (r < 0) {
TESTRPT("failed", r);
}
}
printf("Selecting quarter-size image\n");
r = miselect_resolution(vol, 2);
if (r < 0) {
TESTRPT("miselect_resolution failed", r);
}
/* OK, now try to read the lower-resolution hyperslab */
coords[0] = 0;
coords[1] = 0;
coords[2] = 0;
count[0] = CX/4;
count[1] = CY/4;
count[2] = CZ/4;
{
unsigned int buffer[CX/4][CY/4][CZ/4];
r = miget_voxel_value_hyperslab(vol, MI_TYPE_UINT,
coords, count, buffer);
if (r < 0) {
TESTRPT("failed", r);
}
}
printf("Return to full resolution.\n");
r = miselect_resolution(vol, 0); /* Back to full resolution */
if (r < 0) {
TESTRPT("miselect_resolution failed", r);
}
printf("Flush any remaining thumbnails.\n");
r = miflush_from_resolution(vol, 3);
if (r < 0) {
TESTRPT("failed", r);
}
r = miclose_volume(vol);
if (r < 0) {
TESTRPT("failed", r);
}
if (error_cnt != 0) {
fprintf(stderr, "%d error%s reported\n",
error_cnt, (error_cnt == 1) ? "" : "s");
}
else {
fprintf(stderr, "No errors\n");
}
return (error_cnt);
}
int main(int argc, char **argv)
{
mihandle_t vol;
mivolumeprops_t props;
int r;
micompression_t compression_type;
miboolean_t enable_flag;
int zlib_level;
int depth;
int edge_lengths[MI2_MAX_VAR_DIMS];
int edge_count;
int i;
r = minew_volume_props(&props);
if (r < 0) {
TESTRPT("failed", r);
}
r = miset_props_multi_resolution(props, 1 , 2);
if (r < 0) {
TESTRPT("failed", r);
}
r = miget_props_multi_resolution(props, &enable_flag, &depth);
if (r < 0) {
TESTRPT("failed", r);
}
else {
printf("Multiresolution enabled: %d depth: %d \n", enable_flag, depth);
}
r = miset_props_compression_type(props, MI_COMPRESS_NONE);
if (r < 0) {
TESTRPT("failed", r);
}
else {
printf("Set compression type to %d\n", MI_COMPRESS_NONE);
}
r = miget_props_compression_type(props,&compression_type);
if (r < 0 || compression_type != MI_COMPRESS_NONE) {
TESTRPT("failed", r);
}
else {
printf("Got compression type %d \n", compression_type);
}
r = miset_props_zlib_compression(props,4);
if (r < 0) {
TESTRPT("failed", r);
}
else {
printf("Set zlib level to %d\n", 4);
}
r = miget_props_zlib_compression(props,&zlib_level);
if (r < 0 || zlib_level != 4) {
TESTRPT("failed", r);
}
else {
printf("Got zlib level %d \n", zlib_level);
}
mifree_volume_props(props);
while (--argc > 0) {
r = miopen_volume(*++argv, MI2_OPEN_RDWR, &vol);
if (r < 0) {
TESTRPT("failed", r);
}
r = miget_volume_props(vol, &props);
if (r < 0) {
TESTRPT("failed", r);
}
r = miget_props_blocking(props, &edge_count, edge_lengths,
MI2_MAX_VAR_DIMS);
if (r < 0) {
TESTRPT("failed", r);
}
printf("edge_count %d\n", edge_count);
for (i = 0; i < edge_count; i++) {
printf(" %d", edge_lengths[i]);
}
printf("\n");
mifree_volume_props(props);
miclose_volume(vol);
}
if (error_cnt != 0) {
fprintf(stderr, "%d error%s reported\n",
error_cnt, (error_cnt == 1) ? "" : "s");
}
else {
fprintf(stderr, "No errors\n");
}
return (error_cnt);
}
int
main(void)
{
mihandle_t hvol;
char *name;
int result;
midimhandle_t hdim[NDIMS];
misize_t coords[NDIMS];
misize_t count[NDIMS];
int i,j,k;
struct test {
int r;
int g;
int b;
} voxel;
/* Write data one voxel at a time. */
for (i = 0; i < NDIMS; i++) {
count[i] = 1;
}
result = micreate_dimension("xspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CX, &hdim[0]);
result = micreate_dimension("yspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CY, &hdim[1]);
result = micreate_dimension("zspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CZ, &hdim[2]);
result = micreate_volume("tst-rec.mnc", NDIMS, hdim, MI_TYPE_UINT,
MI_CLASS_UNIFORM_RECORD, NULL, &hvol);
if (result < 0) {
TESTRPT("Unable to create test file", result);
}
result = miset_record_field_name(hvol, 0, "Red");
if (result < 0) {
TESTRPT("miset_record_field_name", result);
}
miset_record_field_name(hvol, 1, "Green");
miset_record_field_name(hvol, 2, "Blue");
miget_record_field_name(hvol, 1, &name);
if (strcmp(name, "Green") != 0) {
TESTRPT("Unexpected label for value 1", 0);
}
mifree_name(name);
miget_record_field_name(hvol, 0, &name);
if (strcmp(name, "Red") != 0) {
TESTRPT("Unexpected label for value 0", 0);
}
mifree_name(name);
miget_record_field_name(hvol, 2, &name);
if (strcmp(name, "Blue") != 0) {
TESTRPT("Unexpected label for value 2", 0);
}
mifree_name(name);
result = micreate_volume_image(hvol);
if (result < 0) {
TESTRPT("micreate_volume_image failed", result);
}
for (i = 0; i < CX; i++) {
for (j = 0; j < CY; j++) {
for (k = 0; k < CZ; k++) {
coords[0] = i;
coords[1] = j;
coords[2] = k;
voxel.r = i;
voxel.g = j;
voxel.b = k;
result = miset_voxel_value_hyperslab(hvol, MI_TYPE_UNKNOWN,
coords, count, &voxel);
if (result < 0) {
TESTRPT("Error writing voxel", result);
}
}
}
}
for (i = 0; i < CX; i++) {
for (j = 0; j < CY; j++) {
for (k = 0; k < CZ; k++) {
coords[0] = i;
coords[1] = j;
coords[2] = k;
result = miget_voxel_value_hyperslab(hvol, MI_TYPE_UNKNOWN,
coords, count, &voxel);
if (result < 0) {
TESTRPT("Error reading voxel", result);
}
if (voxel.r != i || voxel.g != j || voxel.b != k) {
TESTRPT("Data mismatch", 0);
}
}
}
}
miclose_volume(hvol);
if (error_cnt != 0) {
fprintf(stderr, "%d error%s reported\n",
error_cnt, (error_cnt == 1) ? "" : "s");
}
else {
fprintf(stderr, "No errors\n");
}
return (error_cnt);
}
SEXP minc2_apply(SEXP filenames, SEXP fn, SEXP have_mask,
SEXP mask, SEXP mask_value, SEXP rho) {
int result;
mihandle_t *hvol, hmask;
int i, v0, v1, v2, output_index, buffer_index;
unsigned long start[3], count[3];
//unsigned long location[3];
int num_files;
double *xbuffer, *xoutput, **full_buffer;
double *xhave_mask, *xmask_value;
double *mask_buffer;
midimhandle_t dimensions[3];
misize_t sizes[3];
SEXP output, buffer;
//SEXP R_fcall;
/* allocate memory for volume handles */
num_files = LENGTH(filenames);
hvol = malloc(num_files * sizeof(mihandle_t));
Rprintf("Number of volumes: %i\n", num_files);
/* open the mask - if so desired */
xhave_mask = REAL(have_mask);
if (xhave_mask[0] == 1) {
result = miopen_volume(CHAR(STRING_ELT(mask, 0)),
MI2_OPEN_READ, &hmask);
if (result != MI_NOERROR) {
error("Error opening mask: %s.\n", CHAR(STRING_ELT(mask, 0)));
}
}
/* get the value inside that mask */
xmask_value = REAL(mask_value);
/* open each volume */
for(i=0; i < num_files; i++) {
result = miopen_volume(CHAR(STRING_ELT(filenames, i)),
MI2_OPEN_READ, &hvol[i]);
if (result != MI_NOERROR) {
error("Error opening input file: %s.\n", CHAR(STRING_ELT(filenames,i)));
}
}
/* get the file dimensions and their sizes - assume they are the same*/
miget_volume_dimensions( hvol[0], MI_DIMCLASS_SPATIAL,
MI_DIMATTR_ALL, MI_DIMORDER_FILE,
3, dimensions);
result = miget_dimension_sizes( dimensions, 3, sizes );
Rprintf("Volume sizes: %i %i %i\n", sizes[0], sizes[1], sizes[2]);
/* allocate the output buffer */
PROTECT(output=allocVector(REALSXP, (sizes[0] * sizes[1] * sizes[2])));
xoutput = REAL(output);
/* allocate the local buffer that will be passed to the function */
PROTECT(buffer=allocVector(REALSXP, num_files));
xbuffer = REAL(buffer);
//PROTECT(R_fcall = lang2(fn, R_NilValue));
/* allocate first dimension of the buffer */
full_buffer = malloc(num_files * sizeof(double));
/* allocate second dimension of the buffer
- big enough to hold one slice per subject at a time */
for (i=0; i < num_files; i++) {
full_buffer[i] = malloc(sizes[1] * sizes[2] * sizeof(double));
}
/* allocate buffer for mask - if necessary */
if (xhave_mask[0] == 1) {
mask_buffer = malloc(sizes[1] * sizes[2] * sizeof(double));
}
/* set start and count. start[0] will change during the loop */
start[0] = 0; start[1] = 0; start[2] = 0;
count[0] = 1; count[1] = sizes[1]; count[2] = sizes[2];
/* loop across all files and voxels */
Rprintf("In slice \n");
for (v0=0; v0 < sizes[0]; v0++) {
start[0] = v0;
for (i=0; i < num_files; i++) {
if (miget_real_value_hyperslab(hvol[i],
MI_TYPE_DOUBLE,
(misize_t *) start,
(misize_t *) count,
full_buffer[i]) )
error("Error opening buffer.\n");
}
/* get mask - if desired */
if (xhave_mask[0] == 1) {
if (miget_real_value_hyperslab(hmask,
MI_TYPE_DOUBLE,
(misize_t *) start,
(misize_t *) count,
mask_buffer) )
error("Error opening mask buffer.\n");
}
Rprintf(" %d ", v0);
for (v1=0; v1 < sizes[1]; v1++) {
for (v2=0; v2 < sizes[2]; v2++) {
output_index = v0*sizes[1]*sizes[2]+v1*sizes[2]+v2;
buffer_index = sizes[2] * v1 + v2;
/* only perform operation if not masked */
if(xhave_mask[0] == 0
|| (xhave_mask[0] == 1 &&
mask_buffer[buffer_index] > xmask_value[0] -0.5 &&
mask_buffer[buffer_index] < xmask_value[0] + 0.5)) {
for (i=0; i < num_files; i++) {
// location[0] = v0;
// location[1] = v1;
// location[2] = v2;
//SET_VECTOR_ELT(buffer, i, full_buffer[i][index]);
//result = miget_real_value(hvol[i], location, 3, &xbuffer[i]);
xbuffer[i] = full_buffer[i][buffer_index];
//Rprintf("V%i: %f\n", i, full_buffer[i][index]);
}
/* install the variable "x" into environment */
defineVar(install("x"), buffer, rho);
//SETCADDR(R_fcall, buffer);
//SET_VECTOR_ELT(output, index, eval(R_fcall, rho));
//SET_VECTOR_ELT(output, index, test);
/* evaluate the function */
xoutput[output_index] = REAL(eval(fn, rho))[0];
}
else {
xoutput[output_index] = 0;
}
}
}
}
Rprintf("\nDone\n");
/* free memory */
for (i=0; i<num_files; i++) {
miclose_volume(hvol[i]);
free(full_buffer[i]);
}
free(full_buffer);
UNPROTECT(2);
/* return the results */
return(output);
}
int create_4D_image(void)
{
int r;
double start_values[NDIMS+1]={-6.96, -12.453, -9.48, 20.002};
double separations[NDIMS+1]={0.09,0.09,0.09, 1};
midimhandle_t hdim[NDIMS+1];
mihandle_t hvol;
unsigned char *buf = (unsigned char *) malloc(CX * CU * CZ * CY * sizeof(unsigned char));
int i,j;
long count[NDIMS+1];
long start[NDIMS+1];
miboolean_t flag=1;
double min = -1.0;
double max = 1.0;
r = micreate_dimension("xspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CX, &hdim[0]);
r = micreate_dimension("user", MI_DIMCLASS_USER,
MI_DIMATTR_REGULARLY_SAMPLED, CU, &hdim[1]);
r = micreate_dimension("zspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CZ, &hdim[2]);
r = micreate_dimension("yspace", MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED, CY, &hdim[3]);
r = miset_dimension_starts(hdim, NDIMS+1, start_values);
r = miset_dimension_separations(hdim, NDIMS+1, separations);
r = micreate_volume("4D_image.mnc", NDIMS+1, hdim, MI_TYPE_UBYTE,
MI_CLASS_REAL, NULL, &hvol);
/* set slice scaling flag to true */
r = miset_slice_scaling_flag(hvol, flag);
r = micreate_volume_image(hvol);
for (i = 0; i < CX*CU*CZ*CY; i++) {
buf[i] = (unsigned char) i;
}
start[0] = start[1] = start[2] = start[3] = 0;
count[0] = CX; count[1] = CU; count[2] = CZ; count[3] = CY;
r = miset_voxel_value_hyperslab(hvol, MI_TYPE_UBYTE, start, count, buf);
/* Set random values to slice min and max for slice scaling*/
start[0] =start[1]=start[2]=start[3]=0;
for (i=0; i < CX; i++) {
start[0] = i;
for ( j=0; j < CU; j++)
{
start[1] = j;
min += -0.1;
max += 0.1;
r = miset_slice_range(hvol,start,NDIMS+1 , max, min);
}
}
r = miclose_volume(hvol);
return r<0?1:0;
}
/* writes a hyperslab to the output filename, creating the output voluem
to be like the second filename passed in */
void write_minc2_volume(char **output, char **like_filename,
int *start, int *count, double *max_range,
double *min_range, double *slab) {
mihandle_t hvol_like, hvol_new;
midimhandle_t *dimensions_like, *dimensions_new;
unsigned long tmp_count[3];
unsigned long tmp_start[3];
int i;
/* allocate the dimension handles */
dimensions_like = malloc(sizeof(midimhandle_t) * 3);
dimensions_new = malloc(sizeof(midimhandle_t) * 3);
/* read the like volume */
if (miopen_volume(like_filename[0], MI2_OPEN_READ, &hvol_like) < 0 ) {
error("Error opening volume: %s\n", like_filename[0]);
}
/* get dimensions */
if (miget_volume_dimensions( hvol_like, MI_DIMCLASS_SPATIAL, MI_DIMATTR_ALL,
MI_DIMORDER_FILE, 3, dimensions_like ) < 0 ) {
error("Error getting volume dimensions\n");
}
/* copy the dimensions to the new file */
for (i=0; i < 3; i++) {
if (micopy_dimension(dimensions_like[i], &dimensions_new[i]) < 0) {
error ("Error copying dimension %d\n", i);
}
}
/* create the new volume */
if ( micreate_volume(output[0], 3, dimensions_new, MI_TYPE_USHORT,
MI_CLASS_REAL, NULL, &hvol_new) < 0 ) {
error("Error creating volume %s\n", output[0]);
}
if (micreate_volume_image(hvol_new) < 0) {
error("Error creating volume image\n");
}
/* set valid and real range */
miset_volume_valid_range(hvol_new, 65535, 0);
miset_volume_range(hvol_new, max_range[0], min_range[0]);
Rprintf("Range: %f %f\n", max_range[0], min_range[0]);
/* write the buffer */
for (i=0; i < 3; i++) {
tmp_start[i] = (unsigned long) start[i];
tmp_count[i] = (unsigned long) count[i];
}
if (miset_real_value_hyperslab(hvol_new, MI_TYPE_DOUBLE,
(misize_t *) tmp_start,
(misize_t *) tmp_count,
slab) < 0) {
error("Error writing buffer to volume\n");
}
if (miclose_volume(hvol_like) < 0) {
error("Error closing like volume\n");
}
if (miclose_volume(hvol_new) < 0) {
error("Error closing new volume\n");
}
free(dimensions_new);
free(dimensions_like);
return;
}
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);
}
/*
Given a minc filename, return a list containing:
(1) the dimension names
(2) the dimension sizes
(3) and much, much more
*/
SEXP get_volume_info(SEXP filename) {
mihandle_t minc_volume;
midimhandle_t *dimensions;
miclass_t volume_class;
mitype_t volume_type;
int result, i;
int n_dimensions;
misize_t n_dimensions_misize_t;
int n_protects, list_index;
int n_frames;
// variables to hold dim-related info
misize_t dim_sizes[MI2_MAX_VAR_DIMS];
double dim_starts[MI2_MAX_VAR_DIMS];
double dim_steps[MI2_MAX_VAR_DIMS];
double time_offsets[MAX_FRAMES];
double time_widths[MAX_FRAMES];
char *dim_name;
char *dim_units;
char *space_type;
Rboolean time_dim_exists;
static char *dimorder3d[] = { "zspace","yspace","xspace" };
static char *dimorder4d[] = { "time", "zspace","yspace","xspace" };
/* declare R datatypes */
SEXP rtnList, listNames;
SEXP xDimSizes, xDimNames, xDimUnits, xDimStarts, xDimSteps, xTimeWidths, xTimeOffsets;
// start ...
if ( R_DEBUG_mincIO ) Rprintf("get_volume_info: start ...\n");
/* do some initialization */
for (i=0; i < MI2_MAX_VAR_DIMS; ++i){ // set dim info to zeros
dim_sizes[i] = 0;
dim_starts[i] = 0;
dim_steps[i] = 0;
}
// frame-related init
time_dim_exists = FALSE;
for (i=0; i < MAX_FRAMES; ++i) {
time_offsets[i]=999.9;
time_widths[i]=999.9;
}
n_frames = 0;
n_protects = 0; // counter of protected R variables
/* init the return list (include list names) */
PROTECT(rtnList=allocVector(VECSXP, R_RTN_LIST_LEN));
PROTECT(listNames=allocVector(STRSXP, R_RTN_LIST_LEN));
n_protects = n_protects +2;
/* open the existing volume */
result = miopen_volume(CHAR(STRING_ELT(filename,0)), MI2_OPEN_READ, &minc_volume);
/* error on open? */
if (result != MI_NOERROR) {
error("Error opening input file: %s.\n", CHAR(STRING_ELT(filename,0)));
}
/* set the apparent order to something conventional */
// ... first need to get the number of dimensions
if ( miget_volume_dimension_count(minc_volume, MI_DIMCLASS_ANY, MI_DIMATTR_ALL, &n_dimensions) != MI_NOERROR ){
error("Error returned from miget_volume_dimension_count.\n");
}
n_dimensions_misize_t = (misize_t) n_dimensions;
// ... now set the order
if ( R_DEBUG_mincIO ) Rprintf("Setting the apparent order for %d dimensions ... ", n_dimensions);
if ( n_dimensions == 3 ) {
result = miset_apparent_dimension_order_by_name(minc_volume, 3, dimorder3d);
} else if ( n_dimensions == 4 ) {
result = miset_apparent_dimension_order_by_name(minc_volume, 4, dimorder4d);
} else {
error("Error file %s has %d dimensions and we can only deal with 3 or 4.\n", CHAR(STRING_ELT(filename,0)), n_dimensions);
}
if ( result != MI_NOERROR ) {
error("Error returned from miset_apparent_dimension_order_by_name while setting apparent order for %d dimensions.\n", n_dimensions);
}
if ( R_DEBUG_mincIO ) Rprintf("Done.\n");
/* get the volume data class (the intended "real" values) */
if ( miget_data_class(minc_volume, &volume_class) != MI_NOERROR ){
error("Error returned from miget_data_class.\n");
}
/* append to return list ... */
list_index = 0;
SET_VECTOR_ELT(rtnList, list_index, ScalarInteger(volume_class));
SET_STRING_ELT(listNames, list_index, mkChar("volumeDataClass"));
/* print the volume data type (as it is actually stored in the volume) */
if ( miget_data_type(minc_volume, &volume_type) != MI_NOERROR ){
error("Error returned from miget_data_type.\n");
}
/* append to return list ... */
list_index++;
SET_VECTOR_ELT(rtnList, list_index, ScalarInteger(volume_type));
SET_STRING_ELT(listNames, list_index, mkChar("volumeDataType"));
/* retrieve the volume space type (talairach, native, etc) */
result = miget_space_name(minc_volume, &space_type);
if ( result == MI_NOERROR ) { error("Error returned from miget_space_name.\n"); }
/* append to return list ... */
list_index++;
SET_VECTOR_ELT(rtnList, list_index, mkString(space_type));
SET_STRING_ELT(listNames, list_index, mkChar("spaceType"));
/* retrieve the total number of dimensions in this volume */
if ( miget_volume_dimension_count(minc_volume, MI_DIMCLASS_ANY, MI_DIMATTR_ALL, &n_dimensions) != MI_NOERROR ){
error("Error returned from miget_volume_dimension_count.\n");
}
/* append to return list ... */
list_index++;
SET_VECTOR_ELT(rtnList, list_index, ScalarInteger(n_dimensions));
SET_STRING_ELT(listNames, list_index, mkChar("nDimensions"));
/* load up dimension-related information */
//
/* first allocate the R variables */
PROTECT( xDimSizes=allocVector(INTSXP,n_dimensions) );
PROTECT( xDimNames=allocVector(STRSXP,n_dimensions) );
PROTECT( xDimUnits=allocVector(STRSXP,n_dimensions) );
PROTECT( xDimStarts=allocVector(REALSXP,n_dimensions) );
PROTECT( xDimSteps=allocVector(REALSXP,n_dimensions) );
n_protects = n_protects +5;
/* next, load up the midimension struct for all dimensions*/
dimensions = (midimhandle_t *) malloc( sizeof( midimhandle_t ) * n_dimensions );
result = miget_volume_dimensions(minc_volume, MI_DIMCLASS_ANY, MI_DIMATTR_ALL, MI_DIMORDER_APPARENT, n_dimensions, dimensions);
// need to check against MI_ERROR, as "result" will contain nDimensions if OK
if ( result == MI_ERROR ) { error("Error code(%d) returned from miget_volume_dimensions.\n", result); }
/* get the dimension sizes for all dimensions */
result = miget_dimension_sizes(dimensions, n_dimensions_misize_t, dim_sizes);
if ( result != MI_NOERROR ) { error("Error returned from miget_dimension_sizes.\n"); }
/* add to R vector ... */
for (i=0; i<n_dimensions; ++i){
INTEGER(xDimSizes)[i] = dim_sizes[i];
}
list_index++;
SET_VECTOR_ELT(rtnList, list_index, xDimSizes);
SET_STRING_ELT(listNames, list_index, mkChar("dimSizes"));
/* get the dimension START values for all dimensions */
result = miget_dimension_starts(dimensions, MI_ORDER_FILE, n_dimensions, dim_starts);
if ( result == MI_ERROR ) { error("Error returned from miget_dimension_starts.\n"); }
/* add to R vector ... */
for (i=0; i<n_dimensions; ++i){
REAL(xDimStarts)[i] = dim_starts[i];
}
list_index++;
SET_VECTOR_ELT(rtnList, list_index, xDimStarts);
SET_STRING_ELT(listNames, list_index, mkChar("dimStarts"));
/* get the dimension STEP values for all dimensions */
result = miget_dimension_separations(dimensions, MI_ORDER_FILE, n_dimensions, dim_steps);
if ( result == MI_ERROR ) { error("Error returned from miget_dimension_separations.\n"); }
/* add to R vector ... */
for (i=0; i<n_dimensions; ++i){
REAL(xDimSteps)[i] = dim_steps[i];
}
list_index++;
SET_VECTOR_ELT(rtnList, list_index, xDimSteps);
SET_STRING_ELT(listNames, list_index, mkChar("dimSteps"));
/* Loop over the dimensions to grab the remaining info ... */
for( i=0; i < n_dimensions; ++i ){
//
/* get (and print) the dimension names for all dimensions*
... remember that since miget_dimension_name calls strdup which, in turn,
... calls malloc to get memory for the new string -- we need to call "mifree" on
... our pointer to release that memory. */
result = miget_dimension_name(dimensions[i], &dim_name);
// do we have a time dimension?
if ( !strcmp(dim_name, "time") ) {
time_dim_exists = TRUE;
n_frames = ( time_dim_exists ) ? dim_sizes[0] : 0;
}
// store the dimension name and units
SET_STRING_ELT(xDimNames, i, mkChar(dim_name));
mifree_name(dim_name);
result = miget_dimension_units(dimensions[i], &dim_units);
SET_STRING_ELT(xDimUnits, i, mkChar(dim_units));
mifree_name(dim_units);
}
/* add number of frames to return list */
list_index++;
SET_VECTOR_ELT(rtnList, list_index, ScalarInteger(n_frames));
SET_STRING_ELT(listNames, list_index, mkChar("nFrames"));
// add dim names to return list
list_index++;
SET_VECTOR_ELT(rtnList, list_index, xDimNames);
SET_STRING_ELT(listNames, list_index, mkChar("dimNames"));
// add dim units
list_index++;
SET_VECTOR_ELT(rtnList, list_index, xDimUnits);
SET_STRING_ELT(listNames, list_index, mkChar("dimUnits"));
/* get the dimension OFFSETS values for the TIME dimension */
if ( time_dim_exists ) {
PROTECT( xTimeOffsets=allocVector(REALSXP,n_frames) );
n_protects++;
result = miget_dimension_offsets(dimensions[0], n_frames, 0, time_offsets);
if ( result == MI_ERROR ) { error("Error returned from miget_dimension_offsets.\n"); }
/* add to R vector ... */
for (i=0; i < n_frames; ++i) {
REAL(xTimeOffsets)[i] = time_offsets[i];
// if (R_DEBUG_mincIO) Rprintf("Time offset[%d] = %g\n", i, time_offsets[i]);
}
list_index++;
SET_VECTOR_ELT(rtnList, list_index, xTimeOffsets);
SET_STRING_ELT(listNames, list_index, mkChar("timeOffsets"));
/* get the dimension WIDTH values for the TIME dimension */
PROTECT( xTimeWidths=allocVector(REALSXP,n_frames) );
n_protects++;
result = miget_dimension_widths(dimensions[0], MI_ORDER_FILE, n_frames, 0, time_widths);
if ( result == MI_ERROR ) { error("Error returned from miget_dimension_widths.\n"); }
/* add to R vector ... */
for (i=0; i<n_frames; ++i) {
REAL(xTimeWidths)[i] = time_widths[i];
// if (R_DEBUG_mincIO) Rprintf("Time width[%d] = %g\n", i, time_widths[i]);
}
list_index++;
SET_VECTOR_ELT(rtnList, list_index, xTimeWidths);
SET_STRING_ELT(listNames, list_index, mkChar("timeWidths"));
}
// free heap memory
free(dimensions);
/* close volume */
miclose_volume(minc_volume);
/* attach the list component names to the list */
setAttrib(rtnList, R_NamesSymbol, listNames);
/* remove gc collection protection */
UNPROTECT(n_protects);
/* return */
if ( R_DEBUG_mincIO ) Rprintf("get_volume_info: returning ...\n");
return(rtnList);
}
int main(int argc, char **argv)
{
mihandle_t hvol;
int r;
mitype_t data_type;
int length;
static double tstarr[TESTARRAYSIZE] = {
1.1, 2.2, 3.3, 4.4, 5.5, 6.6, 7.7, 8.8, 9.9, 10.10, 11.11
};
double dblarr[TESTARRAYSIZE];
float fltarr[TESTARRAYSIZE];
int intarr[TESTARRAYSIZE];
char valstr[128];
milisthandle_t hlist, h1list;
char pathbuf[256];
char namebuf[256];
char pathbuf1[256];
int count=0;
r = micreate_volume("tst-grpa.mnc", 0, NULL, MI_TYPE_UINT,
MI_CLASS_INT, NULL, &hvol);
if (r < 0) {
TESTRPT("Unable to create test file", r);
return (-1);
}
r = micreate_group(hvol, "/", "test1");
if (r < 0) {
TESTRPT("micreate_group failed", r);
}
r = micreate_group(hvol, "/", "test2");
if (r < 0) {
TESTRPT("micreate_group failed", r);
}
r = micreate_group(hvol, "/", "test3");
if (r < 0) {
TESTRPT("micreate_group failed", r);
}
r = micreate_group(hvol, "/", "test4");
if (r < 0) {
TESTRPT("micreate_group failed", r);
}
r = micreate_group(hvol, "/test2", "stuff2");
if (r < 0) {
TESTRPT("micreate_group failed", r);
}
r = micreate_group(hvol, "/test1", "stuff");
if (r < 0) {
TESTRPT("micreate_group failed", r);
}
r = micreate_group(hvol, "/test1", "otherstuff");
if (r < 0) {
TESTRPT("micreate_group failed", r);
}
r = micreate_group(hvol, "/test1", "theotherstuff");
if (r < 0) {
TESTRPT("micreate_group failed", r);
}
r = micreate_group(hvol, "/test1/theotherstuff", "thisstuff");
if (r < 0) {
TESTRPT("micreate_group failed", r);
}
r = micreate_group(hvol, "/test1/stuff", "hello");
if (r < 0) {
TESTRPT("micreate_group failed", r);
}
r = micreate_group(hvol, "/test1/stuff", "helloleila");
if (r < 0) {
TESTRPT("micreate_group failed", r);
}
r = miset_attr_values(hvol, MI_TYPE_STRING, "/test1/stuff/hello",
"animal", 8, "fruitbat");
if (r < 0) {
TESTRPT("miset_attr_values failed", r);
}
r = miset_attr_values(hvol, MI_TYPE_STRING, "/test1/stuff",
"objtype", 10, "automobile");
if (r < 0) {
TESTRPT("miset_attr_values failed", r);
}
r = miset_attr_values(hvol, MI_TYPE_STRING, "/test3",
"objtype", 10, "automobile");
if (r < 0) {
TESTRPT("miset_attr_values failed", r);
}
r = miset_attr_values(hvol, MI_TYPE_STRING, "/test1/stuff",
"objname", 10, "automobile");
if (r < 0) {
TESTRPT("miset_attr_values failed", r);
}
r = miset_attr_values(hvol, MI_TYPE_DOUBLE, "/test2",
"maxvals", TESTARRAYSIZE, tstarr);
if (r < 0) {
TESTRPT("miset_attr_values failed", r);
}
r = miget_attr_type(hvol, "/test1/stuff/hello", "animal",
&data_type);
if (r < 0) {
TESTRPT("miget_attr_type failed", r);
}
r = miget_attr_length(hvol, "/test1/stuff/hello", "animal",
&length);
if (r < 0) {
TESTRPT("miget_attr_length failed", r);
}
if (data_type != MI_TYPE_STRING) {
TESTRPT("miget_attr_type failed", data_type);
}
if (length != 8) {
TESTRPT("miget_attr_length failed", length);
}
r = midelete_group(hvol, "/test1/stuff", "goodbye");
if (r >= 0) {
TESTRPT("midelete_group failed", r);
}
r = midelete_group(hvol, "/test1/stuff", "hello");
/* This should succeed.
*/
if (r < 0) {
TESTRPT("midelete_group failed", r);
}
r = miget_attr_length(hvol, "/test1/stuff/hello", "animal",
&length);
/* This should fail since we deleted the group.
*/
if (r >= 0) {
TESTRPT("miget_attr_length failed", r);
}
r = miget_attr_values(hvol, MI_TYPE_DOUBLE, "/test2", "maxvals",
TESTARRAYSIZE, dblarr);
if (r < 0) {
TESTRPT("miget_attr_values failed", r);
}
for (r = 0; r < TESTARRAYSIZE; r++) {
if (dblarr[r] != tstarr[r]) {
TESTRPT("miget_attr_values mismatch", r);
}
}
/* Get the values again in float rather than double format.
*/
r = miget_attr_values(hvol, MI_TYPE_FLOAT, "/test2", "maxvals",
TESTARRAYSIZE, fltarr);
if (r < 0) {
TESTRPT("miget_attr_values failed", r);
}
for (r = 0; r < TESTARRAYSIZE; r++) {
if (fltarr[r] != (float) tstarr[r]) {
TESTRPT("miget_attr_values mismatch", r);
fprintf(stderr, "fltarr[%d] = %f, tstarr[%d] = %f\n",
r, fltarr[r], r, tstarr[r]);
}
}
/* Get the values again in int rather than double format.
*/
r = miget_attr_values(hvol, MI_TYPE_INT, "/test2", "maxvals",
TESTARRAYSIZE, intarr);
if (r < 0) {
TESTRPT("miget_attr_values failed", r);
}
for (r = 0; r < TESTARRAYSIZE; r++) {
if (intarr[r] != (int) tstarr[r]) {
TESTRPT("miget_attr_values mismatch", r);
fprintf(stderr, "intarr[%d] = %d, tstarr[%d] = %d\n",
r, intarr[r], r, (int) tstarr[r]);
}
}
r = miget_attr_values(hvol, MI_TYPE_STRING, "/test1/stuff",
"objtype", 128, valstr);
if (r < 0) {
TESTRPT("miget_attr_values failed", r);
}
if (strcmp(valstr, "automobile") != 0) {
TESTRPT("miget_attr_values failed", 0);
}
r = miset_attr_values(hvol, MI_TYPE_STRING, "/test1/stuff",
"objtype", 8, "bicycle");
if (r < 0) {
TESTRPT("miset_attr_values failed on rewrite", r);
}
r = miget_attr_values(hvol, MI_TYPE_STRING, "/test1/stuff",
"objtype", 128, valstr);
if (r < 0) {
TESTRPT("miget_attr_values failed", r);
}
if (strcmp(valstr, "bicycle") != 0) {
TESTRPT("miget_attr_values failed", 0);
}
r = milist_start(hvol, "/", 1, &hlist);
if (r == MI_NOERROR) {
count++;
while (milist_attr_next(hvol, hlist, pathbuf, sizeof(pathbuf),
namebuf, sizeof(namebuf)) == MI_NOERROR) {
printf(" %s %s\n", pathbuf, namebuf);
}
}
milist_finish(hlist);
printf("***************** \n");
r = milist_start(hvol, "/", 1, &h1list);
if (r == MI_NOERROR) {
while( milist_grp_next(h1list, pathbuf1, sizeof(pathbuf1)) == MI_NOERROR) {
printf("%s \n", pathbuf1);
}
}
milist_finish(h1list);
miclose_volume(hvol);
if (error_cnt != 0) {
fprintf(stderr, "%d error%s reported\n",
error_cnt, (error_cnt == 1) ? "" : "s");
}
else {
fprintf(stderr, "No errors\n");
}
return (error_cnt);
}
int main(int argc, char **argv)
{
mihandle_t vol;
midimhandle_t dim[NDIMS];
unsigned int sizes[NDIMS];
unsigned long start[NDIMS];
unsigned long count[NDIMS];
unsigned long howfar[NDIMS];
unsigned long location[NDIMS];
double *buffer,value;
int r = 0;
static char *dimorder[] = {"xspace", "yspace", "zspace"};
printf("Creating image with slice scaling!! \n");
create_test_file();
printf("Opening hyperslab-test2.mnc! \n");
r = miopen_volume("hyperslab-test2.mnc", MI2_OPEN_READ, &vol);
if (r < 0) {
TESTRPT("failed to open image", r);
}
#ifdef APPARENTORDER
/* set the apparent dimension order to be xyz */
r = miset_apparent_dimension_order_by_name(vol, 3, dimorder);
/* get the apparent dimensions and their sizes */
r = miget_volume_dimensions( vol, MI_DIMCLASS_SPATIAL,
MI_DIMATTR_ALL, MI_DIMORDER_APPARENT,
3, dim);
r = miget_dimension_sizes( dim, 3, sizes );
#else
/* get the apparent dimensions and their sizes */
r = miget_volume_dimensions( vol, MI_DIMCLASS_SPATIAL,
MI_DIMATTR_ALL, MI_DIMORDER_FILE,
3, dim);
r = miget_dimension_sizes( dim, 3, sizes );
#endif
if (r == MI_NOERROR) {
printf("Sizes: %d, %d, %d\n", sizes[0], sizes[1], sizes[2]);
}
else {
fprintf(stderr, "Error getting dimension sizes\n");
}
/* try to play with hyperslab functions!! */
start[0] = 4;
start[1] = 3;
start[2] = 5;
howfar[0] = 120;
howfar[1] = 180;
howfar[2] = 110;
count[0] = howfar[0] - start[0];
count[1] = howfar[1] - start[1];
count[2] = howfar[2] - start[2];
/* Alocate memory for the hyperslab*/
buffer = (double *)malloc(count[0] * count[1] * count[2] * sizeof(double));
if (buffer == NULL) {
fprintf(stderr, "Error allocation memory.\n");
exit(-1);
}
/* Get real value hyperslab*/
printf("\n");
printf("Getting a real value hyperslab \n");
printf("Starting at %d, %d, %d \n", start[0], start[1], start[2]);
printf("Extending to %d, %d, %d \n", howfar[0], howfar[1], howfar[2]);
printf("\n");
if (miget_real_value_hyperslab(vol,MI_TYPE_DOUBLE, start, count, buffer)
< 0) {
fprintf(stderr, "Could not get hyperslab.\n");
exit(-1);
}
/* set an arbitrary location to print values from */
location[0] = 70;
location[1] = 100;
location[2] = 104;
printf("Test arbitrary location %d, %d, %d \n",
location[0], location[1], location[2]);
miget_real_value(vol, location, 3, &value);
printf("Test from hyperslab: %f \n",
*( buffer + (location[0] - start[0])*count[1]*count[2] +
(location[1]- start[1]) * count[2] + (location[2]- start[2])));
printf("Test from voxel scaled: %f\n", value);
miget_voxel_value(vol, location, 3, &value);
printf("Test voxel value itself: %f\n", value);
printf("\n");
printf("HMMMMMMMMMM! let's try something else \n");
printf("\n");
/* set another arbitrary location to print values from */
location[0] = 104;
location[1] = 100;
location[2] = 70;
printf("Test arbitrary location %d, %d, %d \n",
location[0], location[1], location[2]);
miget_real_value(vol, location, 3, &value);
printf("Test from hyperslab: %f \n",
*( buffer + (location[0] - start[0])*count[1]*count[2] +
(location[1]- start[1]) * count[2] + (location[2]- start[2])));
printf("Test from voxel scaled: %f\n", value);
miget_voxel_value(vol, location, 3, &value);
printf("Test voxel value itself: %f\n", value);
/* close volume*/
miclose_volume(vol);
if (error_cnt != 0) {
fprintf(stderr, "%d error%s reported\n",
error_cnt, (error_cnt == 1) ? "" : "s");
}
else {
fprintf(stderr, "\n No errors\n");
}
return (error_cnt);
}
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Purpose:
*
*
*
*
*
*/
SEXP write_volume(SEXP filename, SEXP nDimensions,
SEXP dimLengths,
SEXP dimStarts,
SEXP dimSteps,
SEXP volumeDataType,
SEXP volumeRange,
SEXP hSlab) {
mihandle_t minc_volume;
midimhandle_t dim[MI2_MAX_VAR_DIMS];
mivolumeprops_t volume_properties;
int result;
int ndx;
int no_dimensions;
int dim_lengths[MI2_MAX_VAR_DIMS];
double dim_starts[MI2_MAX_VAR_DIMS];
double dim_steps[MI2_MAX_VAR_DIMS];
double volume_range_min, volume_range_max;
int volume_data_type;
// pointer to the volume data
double *hSlab_p;
misize_t hSlab_start[MI2_MAX_VAR_DIMS];
misize_t hSlab_count[MI2_MAX_VAR_DIMS];
// start ...
if ( R_DEBUG_mincIO ) Rprintf("write_volume: start ...\n");
/* init number of dimensions and their respective sizes
... yes, I could get this myself, but it's best set in the calling R code */
no_dimensions = INTEGER(nDimensions)[0];
volume_data_type = INTEGER(volumeDataType)[0];
volume_range_min = REAL(volumeRange)[0];
volume_range_max = REAL(volumeRange)[1];
// init volume data pointer
hSlab_p = REAL(hSlab);
// init lenghts, steps, and starts
for (ndx=0; ndx < no_dimensions; ++ndx) {
dim_lengths[ndx] = INTEGER(dimLengths)[ndx];
hSlab_count[ndx] = INTEGER(dimLengths)[ndx];
dim_starts[ndx] = REAL(dimStarts)[ndx];
dim_steps[ndx] = REAL(dimSteps)[ndx];
}
// set the properties for the new output volume
// ... no compression, no chunking, no multi-resolution, ... nothin fancy
result = minew_volume_props(&volume_properties);
if (result != MI_NOERROR) {
error("write_volume:minew_volume_props: Error setting output volume properties: %s.\n", CHAR(STRING_ELT(filename, 0)));
}
result = miset_props_compression_type(volume_properties, MI_COMPRESS_NONE);
if (result != MI_NOERROR) {
error("write_volume:miset_props_compression_type: Error setting output volume properties: %s.\n", CHAR(STRING_ELT(filename, 0)));
}
result = miset_props_multi_resolution(volume_properties, FALSE, 1);
if (result != MI_NOERROR) {
error("write_volume:miset_props_multi_resolution: Error setting output volume properties: %s.\n", CHAR(STRING_ELT(filename, 0)));
}
/* create the 3 output dimensions in the order Z, Y, X, as the volume
is stored in this order */
// z-dim
result = micreate_dimension("zspace",
MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED,
dim_lengths[0],
&dim[0]);
//
if (result != MI_NOERROR) {
error("write_volume: Error initializing the dimension struct for %s dimension.\n", "zspace");
}
// y-dim
result = micreate_dimension("yspace",
MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED,
dim_lengths[1],
&dim[1]);
//
if (result != MI_NOERROR) {
error("write_volume: Error initializing the dimension struct for %s dimension.\n", "yspace");
}
// x-dim
result = micreate_dimension("xspace",
MI_DIMCLASS_SPATIAL,
MI_DIMATTR_REGULARLY_SAMPLED,
dim_lengths[2],
&dim[2]);
//
if (result != MI_NOERROR) {
error("write_volume: Error initializing the dimension struct for %s dimension.\n", "xspace");
}
// set the start values for each dimension
result = miset_dimension_starts(dim, no_dimensions, dim_starts);
if (result == MI_ERROR) {
error("write_volume: Error setting dimension start values.\n");
}
// set the step values for each dimension
result = miset_dimension_separations(dim, no_dimensions, dim_steps);
if (result == MI_ERROR) {
error("write_volume: Error setting dimension step values.\n");
}
// create the volume structure (no data yet, of course)
result = micreate_volume(CHAR(STRING_ELT(filename, 0)),
no_dimensions,
dim,
volume_data_type,
MI_CLASS_REAL,
volume_properties,
&minc_volume);
//
if (result != MI_NOERROR) {
error("write_volume: Error creating output volume structure: %s.\n", CHAR(STRING_ELT(filename, 0)));
}
// create the path to the image data
result = micreate_volume_image(minc_volume);
//
if (result != MI_NOERROR) {
error("write_volume: Error writing data to volume %s.\n", CHAR(STRING_ELT(filename, 0)));
}
// set valid and real ranges
// ... 0xFFFF=65535=16-bits (unsigned)
miset_volume_valid_range(minc_volume, 0x7FFF, 0);
miset_volume_range(minc_volume, volume_range_max, volume_range_min);
// write hyperslab (entire volume)
hSlab_start[0] = hSlab_start[1] = hSlab_start[2] = 0;
if ( R_DEBUG_mincIO ) Rprintf("hSlab_count [0..2] = %d, %d, %d\n",
hSlab_count[0], hSlab_count[1], hSlab_count[2]);
result = miset_real_value_hyperslab(minc_volume, MI_TYPE_DOUBLE,
hSlab_start,
hSlab_count,
hSlab_p);
if ( result != MI_NOERROR ) {
error("Error in miset_real_value_hyperslab: %s.\n", CHAR(STRING_ELT(filename, 0)));
}
// free resources
//
// in the current version of minc (libsrc2/volume.c), these volume properties
// as well as the dimension handles are already freed by the miclose_volume function.
//
//mifree_volume_props(volume_properties); // free the property list
//for ( ndx=0; ndx<no_dimensions; ++ndx) { // free the dimhandles
// mifree_dimension_handle(dim[ndx]);
//}
// close new volume
result = miclose_volume(minc_volume);
if (result != MI_NOERROR) {
error("write_volume: Error closing newly created volume %s.\n", CHAR(STRING_ELT(filename, 0)));
}
// done, return NULL
if ( R_DEBUG_mincIO ) Rprintf("write_volume: returning ...\n");
return(R_NilValue);
}
