bool check_same_dimensions(vector<mihandle_t> volumes){
vector<mihandle_t>::iterator volume_iterator;
midimhandle_t first_dims[3];
misize_t first_sizes[3];
midimhandle_t dimensions[3];
misize_t sizes[3];
miget_volume_dimensions(volumes[0], MI_DIMCLASS_SPATIAL,
MI_DIMATTR_ALL, MI_DIMORDER_FILE,
3, first_dims);
miget_dimension_sizes( first_dims, 3, first_sizes);
bool all_same_size = true;
for(volume_iterator = volumes.begin() + 1;
volume_iterator != volumes.end() && all_same_size;
++volume_iterator){
miget_volume_dimensions(*volume_iterator, MI_DIMCLASS_SPATIAL,
MI_DIMATTR_ALL, MI_DIMORDER_FILE,
3, dimensions);
miget_dimension_sizes(dimensions, 3, sizes);
all_same_size =
all_same_size &&
sizes[0] == first_sizes[0] &&
sizes[1] == first_sizes[1] &&
sizes[2] == first_sizes[2];
}
return(all_same_size);
}
vector<misize_t> get_volume_dimensions(mihandle_t volume){
midimhandle_t dimensions[3];
misize_t sizes[3];
vector<misize_t> volume_dimensions(3, 0);
int success = miget_volume_dimensions(volume, MI_DIMCLASS_SPATIAL,
MI_DIMATTR_ALL, MI_DIMORDER_FILE,
3, dimensions);
if(success == MI_ERROR){
stop("Couldn't read volume dimensions");
}
success = miget_dimension_sizes(dimensions, 3, sizes);
if(success != MI_NOERROR){
stop("Couldn't read dimension sizes");
}
for(int i = 0; i < 3; ++i){
volume_dimensions[i] = sizes[i];
}
return(volume_dimensions);
}
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);
}
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;
}
/* open_minc_files: given a vector of filenames, open the volumes and
* returns the dimhandles */
mihandle_t* open_minc_files(SEXP filenames,
misize_t *sizes) {
int num_files, i, result;
midimhandle_t dimensions[3];
mihandle_t *hvol;
num_files = LENGTH(filenames);
hvol = malloc(num_files * sizeof(mihandle_t));
/* open all the files */
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 dimension size - assume it's the same for all volumes */
result = miget_volume_dimensions( hvol[0], MI_DIMCLASS_SPATIAL,
MI_DIMATTR_ALL, MI_DIMORDER_FILE,
3, dimensions );
if (result == MI_ERROR) {
error("Error getting dimensions\n");
}
result = miget_dimension_sizes(dimensions, 3, sizes);
Rprintf("Sizes: %d %d %d\n", sizes[0], sizes[1], sizes[2]);
if (result == MI_ERROR) {
error("Error getting dimension sizes\n");
}
return(hvol);
}
vector<double> get_step_sizes(mihandle_t volume){
midimhandle_t dimensions[3];
double steps[3];
vector<double> step_sizes(3, 0);
int success = miget_volume_dimensions(volume, MI_DIMCLASS_SPATIAL,
MI_DIMATTR_ALL, MI_DIMORDER_FILE,
3, dimensions);
if(success == MI_ERROR){
stop("Couldn't read volume dimensions");
}
success = miget_dimension_separations(dimensions, MI_ORDER_FILE
, 3, steps);
if(success != MI_NOERROR)
stop("Couldn't read volume step sizes");
for(int i = 0; i < 3; ++i)
step_sizes[i] = steps[i];
return(step_sizes);
}
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);
}
/*
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);
}
static int
check_dims(mihandle_t vol, midimhandle_t dim[])
{
int i;
int r;
int n;
mihandle_t vol_tmp;
midimhandle_t dim_tmp[NDIMS];
double offsets[100];
for (i = 0; i < CT; i++) {
double tmp = -1;
r = miget_dimension_offsets(dim[0], 1, i, &tmp);
if (r < 0) {
TESTRPT("failed", r);
}
if ((i * i) + 100.0 != tmp) {
TESTRPT("bad value", i);
}
}
r = miget_dimension_offsets(dim[1], CX, 0, offsets);
if (r < 0) {
TESTRPT("failed", r);
}
for (i = 0; i < CX; i++) {
if (offsets[i] != XSTART + (i * XSTEP)) {
TESTRPT("bad value", i);
}
}
r = miget_dimension_offsets(dim[2], CY, 0, offsets);
if (r < 0) {
TESTRPT("failed", r);
}
for (i = 0; i < CY; i++) {
if (offsets[i] != YSTART + (i * YSTEP)) {
TESTRPT("bad value", i);
}
}
r = miget_dimension_offsets(dim[3], CZ, 0, offsets);
if (r < 0) {
TESTRPT("failed", r);
}
for (i = 0; i < CZ; i++) {
if (offsets[i] != ZSTART + (i * ZSTEP)) {
TESTRPT("bad value", i);
}
}
r = miget_volume_dimension_count(vol, MI_DIMCLASS_SPATIAL, MI_DIMATTR_ALL,
&n);
if (r < 0) {
TESTRPT("failed", r);
}
if (n != NDIMS-1) {
TESTRPT("wrong number of spatial dimensions", n);
}
r = miget_volume_dimension_count(vol, MI_DIMCLASS_ANY, MI_DIMATTR_ALL,
&n);
if (r < 0) {
TESTRPT("failed", r);
}
if (n != NDIMS) {
TESTRPT("wrong number of dimensions", n);
}
r = miget_volume_dimension_count(vol, MI_DIMCLASS_TIME, MI_DIMATTR_ALL,
&n);
if (r < 0) {
TESTRPT("failed", r);
}
if (n != 1) {
TESTRPT("wrong number of time dimensions", n);
}
for (i = 0; i < NDIMS; i++) {
miboolean_t flag_value;
r = miget_dimension_sampling_flag(dim[i], &flag_value);
if (r < 0) {
TESTRPT("error getting sampling flag", r);
}
else if (flag_value != (i == 0)) {
TESTRPT("wrong value for sampling flag", i);
}
}
r = miget_volume_dimensions(vol, MI_DIMCLASS_ANY, MI_DIMATTR_ALL,
MI_DIMORDER_FILE, NDIMS, dim_tmp);
if (r < 0) {
TESTRPT("failed to get dimensions", r);
}
for (i = 0; i < NDIMS; i++) {
vol_tmp = NULL;
r = miget_volume_from_dimension(dim_tmp[i], &vol_tmp);
if (r < 0) {
TESTRPT("failed to get volume from dimension", r);
}
else if (vol_tmp != vol) {
TESTRPT("wrong volume returned", i);
}
}
return (error_cnt);
}
t_vol *init_get_volume_from_minc_file(char *path)
{
t_vol *volume;
int result;
volume = malloc(sizeof(*volume));
volume->path = path;
volume->dim_nb = 3;
if (volume->path == NULL)
return (NULL);
// open the minc file
if ((result = miopen_volume(volume->path, MI2_OPEN_READ, &volume->minc_volume)) != MI_NOERROR)
{
ERROR("Error opening input file: %d.", result);
return (NULL);
}
if ((result = miget_volume_dimension_count(volume->minc_volume, 0, 0, &volume->dim_nb)) != MI_NOERROR)
{
ERROR("Error getting number of dimensions: %d.", result);
return (NULL);
}
volume->dimensions = malloc(volume->dim_nb * sizeof(*volume->dimensions));
volume->starts = malloc(volume->dim_nb * sizeof(*volume->starts));
volume->steps = malloc(volume->dim_nb * sizeof(*volume->steps));
volume->size = malloc(volume->dim_nb * sizeof(*volume->size));
volume->dim_name = malloc(volume->dim_nb * sizeof(*volume->dim_name));
// get the volume dimensions
if ((result = miget_volume_dimensions(volume->minc_volume, MI_DIMCLASS_SPATIAL, MI_DIMATTR_ALL,
MI_DIMORDER_FILE, volume->dim_nb, volume->dimensions)) == MI_ERROR)
{
ERROR("Error getting dimensions: %d.", result);
return (NULL);
}
// get the size of each dimensions
if ((result = miget_dimension_sizes(volume->dimensions, volume->dim_nb, volume->size)) != MI_NOERROR)
{
ERROR("Error getting dimensions size: %d.", result);
return (NULL);
}
if ((result = miget_dimension_starts(volume->dimensions, 0, volume->dim_nb, volume->starts)) != MI_NOERROR)
{
ERROR("Error getting dimensions start: %d.", result);
return (NULL);
}
if ((result = miget_dimension_separations(volume->dimensions, 0, volume->dim_nb, volume->steps)) != MI_NOERROR)
{
ERROR("Error getting dimensions steps: %d.", result);
return (NULL);
}
if (miget_dimension_name (volume->dimensions[0], &volume->dim_name[0]) != MI_NOERROR ||
miget_dimension_name (volume->dimensions[1], &volume->dim_name[1]) != MI_NOERROR ||
miget_dimension_name (volume->dimensions[2], &volume->dim_name[2]))
{
ERROR("Error getting dimensions name.");
return (NULL);
}
// get slices_max
volume->slices_max = get_slices_max(volume);
volume->next = NULL;
return (volume);
}
/* 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;
}
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 main ( void )
{
mihandle_t vol;
int r = 0;
midimhandle_t dim[NDIMS];
misize_t lengths[NDIMS];
midimhandle_t copy_dim[NDIMS];
misize_t coords[NDIMS];
misize_t count[NDIMS];
int i, j;
unsigned char * Atmp;
midimclass_t dimension_class;
int ndims;
Atmp = ( unsigned char * ) malloc ( CX * CY * CZ * sizeof ( unsigned char ) );
create_test_file();
printf ( " \n" );
printf ( "Opening vector-dimension file!\n" );
printf ( " \n" );
r = miopen_volume ( "example_vector2.mnc", MI2_OPEN_READ, &vol );
if ( r < 0 ) {
TESTRPT ( "failed to open vector_dimension volume", r );
}
r = miget_volume_dimension_count ( vol, MI_DIMCLASS_ANY, MI_DIMATTR_REGULARLY_SAMPLED, &ndims );
if ( r < 0 ) {
TESTRPT ( "failed to get number of dimensions", r );
}
printf ( "Total number of dimensions : %d \n", ndims );
r = miget_volume_dimensions ( vol, MI_DIMCLASS_ANY, MI_DIMATTR_REGULARLY_SAMPLED, MI_DIMORDER_FILE, NDIMS, dim );
if ( r < 0 ) {
TESTRPT ( "Could not get dimension handles from volume", r );
}
r = miget_dimension_sizes ( dim, NDIMS, lengths );
if ( r < 0 ) {
TESTRPT ( " more trouble", r );
}
printf ( "Dimension Size in file order : " );
for ( i = 0; i < NDIMS; i++ ) {
printf ( " %lld ", lengths[i] );
}
printf ( " \n" );
for ( i = 0; i < NDIMS; i++ ) {
r = miget_dimension_class ( dim[i], &dimension_class );
if ( r < 0 ) {
TESTRPT ( "failed to get dimension class", r );
}
if ( dimension_class == MI_DIMCLASS_RECORD ) {
printf ( "Dim class RECORD present check dim name for *vector_dimension*\n" );
}
}
printf ( "Let's get the first 10 data values of each vector component (file order) \n" );
coords[0] = coords[1] = coords[2] = 0;
count[0] = CZ;
count[1] = CY;
count[2] = CX;
count[3] = 1;
printf ( " FILE ORDER --> zspace, yspace, xspace, vector_dimension \n" );
for ( i = 0; i < 3; i++ ) {
printf ( "Vector Componenet %d \n", i + 1 );
coords[3] = i;
r = miget_voxel_value_hyperslab ( vol, MI_TYPE_UBYTE, coords, count, Atmp );
if ( r < 0 ) {
TESTRPT ( "Failed to operate hyperslab function", r );
}
for ( j = 0; j < 10; j++ ) {
printf ( " %u ", Atmp[j] );
}
printf ( " \n" );
}
printf ( "APPARENT ORDER --> vector_dimension, zspace, yspace, xspace\n" );
// Set the apparent dimension order
copy_dim[0] = dim[3];
copy_dim[1] = dim[0];
copy_dim[2] = dim[1];
copy_dim[3] = dim[2];
r = miset_apparent_dimension_order ( vol, NDIMS, copy_dim );
if ( r < 0 ) {
TESTRPT ( "failed to set apparent order", r );
}
coords[1] = coords[2] = coords[3] = 0;
count[0] = 1; //must always be one
count[1] = CZ;
count[2] = CY;
count[3] = CZ;
printf ( "APPARENT ORDER SET \n" );
for ( i = 0; i < 3; i++ ) {
printf ( "Vector Componenet %d \n", i + 1 );
coords[0] = i;
r = miget_voxel_value_hyperslab ( vol, MI_TYPE_UBYTE, coords, count, Atmp );
if ( r < 0 ) {
TESTRPT ( "Failed to operate hyperslab function", r );
}
for ( j = 0; j < 10; j++ ) {
printf ( " %u ", Atmp[j] );
}
printf ( " \n" );
}
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 );
}
void MINCResource::Load() {
if (loaded) return;
int result = miopen_volume(file.c_str(), MI2_OPEN_READ, &handle);
if (result != MI_NOERROR) {
logger.warning << "Error opening the MINC input file: " << file << logger.end;
return;
}
// char** names = new char*[3];
// names[0] = "x_space";
// names[1] = "y_space";
// names[2] = "z_space";
// miset_apparent_dimension_order_by_name(handle, 3, names);
int count;
miget_volume_voxel_count(handle, &count);
logger.info << "voxel count: " << count << logger.end;
// atomic type of the resulting texture (float, int)
miclass_t klass;
miget_data_class(handle, &klass);
logger.info << "data class: " << klass << logger.end;
// data type of a voxel (float, uchar, ...)
// convert this type into class type by scaling.
mitype_t type;
miget_data_type(handle, &type);
logger.info << "voxel type: " << type << logger.end;
misize_t vsize;
miget_data_type_size(handle, &vsize);
logger.info << "voxel size in bytes: " << vsize << logger.end;
midimhandle_t dims[3];
result = miget_volume_dimensions(handle, MI_DIMCLASS_SPATIAL,
MI_DIMATTR_ALL, MI_DIMORDER_FILE,
3, dims);
if (result != 3) {
logger.warning << "Only three spatial dimensions supported. Volume has " << result << logger.end;
return;
}
w = h = d = 0;
// hack: in our files dimensions are given in z,y,x order, so we reverse it.
miget_dimension_size(dims[0], &w);
miget_dimension_size(dims[1], &h);
miget_dimension_size(dims[2], &d);
// midimhandle_t* dims_app = new midimhandle_t[3];
// dims_app[0] = dims[2];
// dims_app[1] = dims[1];
// dims_app[2] = dims[0];
// miset_apparent_dimension_order (handle, 3, dims_app);
logger.info << "dimensions: " << w << " x " << h << " x " << d << logger.end;
// count records
int recs = 0;
miget_record_length(handle, &recs);
logger.info << "record length: " << recs << logger.end;
// count labels
int lbls = 0;
miget_number_of_defined_labels(handle, &lbls);
logger.info << "# of labels: " << lbls << logger.end;
// count attributes
milisthandle_t lhandle;
milist_start(handle, "", 0, &lhandle);
char* path = new char[255];
char* name = new char[255];
while (milist_attr_next(handle, lhandle, path, 255, name, 255) == MI_NOERROR) {
logger.info << "path: " << string(path) << " name: " << string(name) << logger.end;
}
milist_finish(lhandle);
delete path;
delete name;
// char* nm;
// miget_dimension_name(dims[2], &nm);
// string hest(nm);
// mifree_name(nm);
// logger.info << "dimension name: " << hest << logger.end;
char* space_name;
miget_space_name(handle, &space_name);
logger.info << "space name: " << string(space_name) << logger.end;
mifree_name(space_name);
loaded = true;
}
