/*
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 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:
*
* Convert world coordinates to a vector of voxel coords
*
* NOTE:
* (1) 0-relative voxel coordinates are being returned
* (2) output voxel coordinates are in volume order, which we are forcing to be (t)zyx
* (3) input world coordinates are in xyz order
* (4) if the volume has 4D, then 4 voxel coords are returned, else 3 of 'em
*
* * * * * * * * * * * * * */
SEXP convert_world_to_voxel_mincIO(SEXP filename, SEXP worldCoords) {
int result, ndx;
int n_dimensions;
mihandle_t minc_volume;
double voxel_coords[MI2_MAX_VAR_DIMS];
double world_coords[MI2_3D];
static char *dimorder3d[] = { "zspace","yspace","xspace" };
static char *dimorder4d[] = { "time", "zspace","yspace","xspace" };
SEXP output;
// start ...
if ( R_DEBUG_mincIO ) Rprintf("convert_world_to_voxel: start ...\n");
// init the world coordinates
for ( ndx=0; ndx < MI2_3D; ++ndx ) {
world_coords[ndx] = REAL(worldCoords)[ndx];
}
/* open the volume */
result = miopen_volume(CHAR(STRING_ELT(filename,0)), MI2_OPEN_READ, &minc_volume);
//
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");
}
/* ... now set the order */
if ( R_DEBUG_mincIO ) Rprintf("convert_world_to_voxel: 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");
// do the call
miconvert_world_to_voxel(minc_volume, world_coords, voxel_coords);
// allocate output vector and then copy the results into it
PROTECT(output=allocVector(REALSXP, n_dimensions));
for ( ndx=0; ndx < n_dimensions; ++ndx ) {
REAL(output)[ndx] = voxel_coords[ndx];
}
// remove protection and return vector
UNPROTECT(1);
if ( R_DEBUG_mincIO ) Rprintf("convert_world_to_voxel: returning ...\n");
return(output);
}
